#***ImmunoSeq Version 1.0***
#Config File: /home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/3F12_C+57_02162010.in
#Spectrum Files:
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1250_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_450_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1400_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1025_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_725_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1075_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_575_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_900_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_525_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_600_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1050_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_575_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1050_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_750_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1225_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1400_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1325_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1150_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_450_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_575_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1100_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1250_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1175_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1450_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_625_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1200_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_850_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1525_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_800_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_600_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_950_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_650_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1350_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_675_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_400_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_800_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1300_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1125_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1300_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_900_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_900_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_650_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_750_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_500_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1000_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_550_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_700_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1025_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_500_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1550_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1300_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1275_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1375_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1400_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_975_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1350_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_950_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_675_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1575_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_400_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_475_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1375_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_875_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1200_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1250_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1475_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_475_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_825_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_925_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_425_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_775_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_775_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1275_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_425_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1425_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1450_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_425_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1200_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_475_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1175_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_825_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_650_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1125_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_700_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1325_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_750_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1425_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_1000_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_525_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_925_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_825_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1225_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_1000_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_975_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_500_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_850_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_800_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_850_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_725_0.mgf
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1075_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Trypsin_0_0_675_0.mgf
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Other_0_0_450_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_775_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_LTQ/3F12_LTQ_Chymotrypsin_0_0_1050_0.mgf
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_450_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Trypsin_0_0_1125_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_500_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Other_0_0_1275_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Other_0_0_775_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_1250_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Other_0_0_600_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Trypsin_0_0_800_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Trypsin_0_0_500_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_625_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Other_0_0_1375_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_650_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_875_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Trypsin_0_0_875_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_1425_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Trypsin_0_0_625_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_1275_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Trypsin_0_0_1025_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_900_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Other_0_0_1475_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_975_0.mgf
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/Spectra/New_02162010/Cluster_Orbi/3F12_Orbi_Chymotrypsin_0_0_950_0.mgf
#Inspect Data (1703): /home/natalie/Projects/MySVNProjects/Inspect/trunk/
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1250_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1250_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_450_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_450_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1400_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1400_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1025_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1025_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_725_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_725_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1075_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1075_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_575_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_575_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_900_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_900_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_525_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_525_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_600_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_600_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1050_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1050_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_575_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_575_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1050_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1050_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_750_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_750_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1225_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1225_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1400_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1400_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1325_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1325_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1150_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1150_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_450_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_450_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_575_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_575_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1100_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1100_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1250_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1250_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1175_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1175_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1450_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1450_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_625_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_625_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1200_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1200_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_850_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_850_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1525_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1525_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_800_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_800_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_600_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_600_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_950_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_950_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_650_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_650_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1350_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1350_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_675_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_675_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_400_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_400_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_800_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_800_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1300_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1300_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1125_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1125_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1300_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1300_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_900_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_900_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_900_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_900_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_650_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_650_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_750_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_750_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_500_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_500_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1000_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1000_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_550_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_550_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_700_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_700_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1025_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1025_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_500_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_500_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1550_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1550_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1300_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1300_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1275_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1275_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1375_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1375_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1400_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1400_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_975_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_975_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1350_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1350_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_950_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_950_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_675_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_675_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_400_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_400_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_475_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_475_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_875_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_875_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1200_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1200_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1250_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1250_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_425_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_425_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1175_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1175_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_825_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_825_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_650_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_650_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1125_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1125_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_700_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_700_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_525_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_525_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_925_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_925_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1225_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1225_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1000_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1000_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_500_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_500_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_850_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_850_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_800_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_800_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_850_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_850_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_725_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_725_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1375_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1375_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_875_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_875_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1150_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1150_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1150_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1150_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_525_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_525_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1025_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1025_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1275_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1275_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_975_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_975_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_700_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_700_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_625_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_625_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1225_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1225_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_950_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_950_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1425_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1425_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1075_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1075_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_675_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_675_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_600_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_600_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_450_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_450_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_775_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_775_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1050_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1050_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1350_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1350_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1100_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_1100_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1475_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Other_0_0_1475_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_925_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_925_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1075_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Trypsin_0_0_1075_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_550_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_LTQ_Chymotrypsin_0_0_550_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_600_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_600_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_1400_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_1400_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_425_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_425_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_1250_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_1250_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_1100_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_1100_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Other_0_0_675_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Other_0_0_675_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_1025_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_1025_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_1175_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Trypsin_0_0_1175_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_850_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_850_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_575_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_575_0_AA_freemod.out
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_475_0_AA.in:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/InspectFiles_02162010/3F12_Orbi_Chymotrypsin_0_0_475_0_AA_freemod.out
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#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1275_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_450_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1375_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1150_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_1475_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_650_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_900_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_1375_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_750_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1400_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_525_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1500_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1250_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1050_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1000_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_1325_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_950_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_950_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1550_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_400_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_825_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_700_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1100_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_550_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_575_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_500_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1425_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_725_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_525_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_675_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_725_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_1025_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_775_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1475_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1025_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1000_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1200_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_1250_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_900_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_700_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_925_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_875_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_975_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_400_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_850_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_650_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_1075_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_825_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_475_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_1175_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_625_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Chymotrypsin_0_0_975_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_750_0.prm
#/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_600_0.prm
#Parameters:
# Seed Coverage: 1.0
# Min Template Likelihood: 1.0
# SpecAlignment SCORE Cutoff: 71.0
# Min peaks spec aligned: 4
# MaxAlignedSpectra kept per Seed: 5
# Min HMM Match State Score: 10.717373334221746
# Min Votes to consider a new match: 2
# HMM Score worsening multiplier: 1.2
# HMM Match Miss Penalty: 3.33686625410141
# Fixed Mod on C:57.0

(LEFT)Round: 0 for seed: QSGAELMKPGASVKLSCKATGYTFTGYWIEWVKQRPGHGLEWIGE
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_700_0.prm:24
 Score: 148.611, AlignedPeaks: 537082 665138 752152 809068 880145 1009180 1122217 1253256 1381336 
0 146572 163328 173826 275717 276499 277165 295179 296091 390195 409011 425965 426259 447333 447751 518197 519217 535954 537082 548090 551918 555002 561337 590298 608266 615782 647245 665138 677833 708576 711203 717292 717830 734245 752152 783564 809068 837912 847428 862299 880145 904072 951595 952013 969097 973087 973381 990364 992285 997531 1009180 1010371 1018416 1103290 1122217 1140154 1225208 1225520 1252774 1253256 1253545 1381336 
15.0 7.322 0.724 0.013 0.64 0.269 11.334 2.434 19.117 13.212 18.716 5.81 5.223 6.055 4.251 0.347 12.175 1.122 18.896 2.809 0.612 1.699 4.066 5.509 3.501 0.963 8.687 14.021 0.667 2.933 0.733 0.719 1.646 9.689 12.376 0.051 8.823 3.886 0.695 17.805 12.719 0.016 4.367 4.663 0.191 3.929 2.718 15.855 0.737 1.657 13.158 1.319 2.839 19.451 26.409 1.147 1.318 1.379 9.865 12.209 11.403 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1175_0.prm:29
 Score: 147.39899999999997, AlignedPeaks: 537136 665243 752178 809101 880178 1009264 1122393 1253273 1381406 1478511 
0 326330 364134 380858 391617 408604 409142 410099 423561 425660 426994 428682 431026 444577 454150 472169 519301 537136 553889 559307 658084 662910 665243 713176 745340 749835 752178 809101 826262 873249 878012 880178 881436 963205 991242 1005511 1007181 1009264 1017302 1089139 1098566 1122393 1193382 1201475 1229444 1253273 1323709 1334543 1342621 1343373 1379311 1381406 1388640 1399414 1444124 1452945 1453668 1470409 1471644 1478511 1507558 1525583 1542760 1559507 1560736 1599721 1602010 1606514 1635588 1638669 1651827 1655626 1668929 1686669 1688935 1693529 1699357 1717422 1751551 1766636 1769608 1792561 1794774 1812528 1814758 1879676 1897695 1920819 1939491 1942703 1943177 1960228 1970987 1987711 2025515 
15.0 3.048 3.506 6.238 9.524 22.829 25.057 14.764 4.023 8.127 3.058 3.886 6.752 7.956 1.522 4.719 0.053 13.553 3.067 7.704 1.485 1.732 16.874 0.722 1.985 0.499 16.361 12.241 0.619 3.096 0.169 18.308 1.503 0.17 0.278 0.881 2.279 16.08 0.726 0.884 3.967 14.34 4.879 0.959 8.059 15.186 1.039 0.606 9.572 1.162 2.205 17.956 3.08 2.078 2.854 2.478 1.634 3.469 19.907 6.5 1.666 2.455 5.601 0.568 7.072 15.312 0.024 8.158 3.192 2.84 0.844 2.116 2.149 19.922 0.108 6.267 1.242 1.777 1.466 2.915 1.161 13.976 1.191 4.78 22.649 0.299 1.888 5.009 1.983 22.529 19.671 11.974 5.517 1.311 1.73 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1225_0.prm:12
 Score: 136.947, AlignedPeaks: 537118 665211 752209 809287 880221 1009185 1122430 1253340 1381513 1478589 
0 206011 312151 329391 348113 364134 365225 380876 383282 409102 411148 415575 416632 417090 426212 427261 434321 454138 468187 472286 521335 530147 536469 537118 539297 551794 553874 554582 562866 585208 652324 658263 665211 716168 752209 775153 809287 826316 844309 862227 867420 880221 954129 972210 994101 995335 1007425 1008277 1009185 1067307 1082121 1100179 1120318 1122430 1197522 1199564 1207761 1208019 1208444 1242431 1242856 1243114 1251311 1253340 1328448 1330604 1346468 1381513 1390133 1399494 1433225 1433754 1441691 1442599 1456775 1478589 1493672 1494682 1496746 1539528 1570651 1583438 1588648 1606715 1624559 1641586 1659734 1670347 1675723 1698713 1711447 1734708 1764694 1768823 1774835 1785692 1792620 1913796 2023614 2024663 2033786 2041774 2067594 2070000 2085650 2086741 
15.0 4.334 7.5 1.505 0.998 1.45 0.926 1.436 3.622 11.773 4.41 5.396 9.477 9.477 14.101 8.563 6.001 10.643 3.64 7.563 4.959 4.597 3.146 9.333 8.747 0.587 2.03 3.91 0.231 0.775 0.472 5.619 16.047 0.961 16.196 0.236 10.825 0.771 4.294 1.378 1.513 19.149 3.057 4.109 1.302 2.253 1.357 7.404 14.752 2.149 4.452 0.833 8.212 15.696 8.503 0.107 0.716 0.571 0.774 0.073 1.926 1.174 0.987 14.08 13.315 4.579 1.055 11.27 2.085 1.699 1.986 4.452 8.154 9.964 0.278 9.599 3.11 0.231 0.797 2.718 21.035 7.636 1.134 12.461 3.32 8.391 7.77 3.313 0.571 15.001 4.096 3.2 0.623 1.933 0.492 1.664 1.728 5.626 2.646 0.971 0.726 0.05 2.307 2.613 0.9 0.868 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_700_0.prm:16
 Score: 134.309, AlignedPeaks: 537215 665259 752261 809148 880283 1009327 1122525 1253169 1381648 
0 277175 277729 296143 390255 392271 409180 424209 442051 450681 519267 532358 536559 537215 552315 555355 572386 590450 608585 615702 647352 665259 677217 686025 708829 711684 714260 717149 722441 734298 752261 809148 827189 847343 847959 861552 862380 879130 880283 894254 899589 904385 948977 975527 986224 990363 1004182 1007387 1009327 1010377 1013319 1018652 1027204 1035377 1068676 1103504 1121929 1122525 1253169 1381648 
15.0 14.501 9.016 14.459 17.777 0.741 14.89 5.702 0.352 1.036 11.058 0.552 1.788 19.891 0.904 2.438 3.851 10.216 4.199 0.059 7.189 12.611 0.098 1.529 1.998 1.847 3.311 1.101 1.017 9.682 9.829 8.096 2.856 1.157 2.422 0.616 18.16 1.332 12.087 0.801 3.108 0.583 0.098 8.507 0.391 10.147 1.99 2.432 12.051 0.75 0.384 1.928 1.822 0.334 0.534 14.403 5.16 19.376 10.368 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:46
 Score: 134.02900000000002, AlignedPeaks: 553105 681212 768285 825479 896198 1025233 1138432 1269394 1397448 1494381 
0 127741 162640 174083 244880 263012 277103 278038 294170 310860 312061 315240 330985 332346 365214 402355 411205 425044 425507 429190 440812 441441 443043 459090 459710 460335 472220 478089 534841 535473 553105 554290 568294 568853 570717 588108 600215 681212 685330 703532 768285 807171 816333 816940 824739 825479 834478 844275 869461 886112 896198 929495 945740 947621 986217 994056 995054 1008997 1025233 1040138 1040844 1049306 1058499 1076693 1085276 1110462 1133297 1137797 1138432 1147566 1165609 1186467 1189690 1198221 1204525 1238454 1241579 1253187 1269394 1273543 1287383 1291544 1354521 1366629 1369568 1384020 1385884 1386443 1387663 1397448 1401595 1415411 1419264 1419896 1476648 1482516 1494381 1495646 1511694 1513296 1513925 1529230 1529693 1543531 1561704 1622391 1642638 1660608 1691725 1709857 1780654 1808865 1936726 
15.0 8.487 2.59 1.556 6.006 6.842 0.256 3.349 9.292 6.761 18.01 4.215 3.038 0.293 1.187 1.596 0.362 19.277 16.021 1.387 1.243 1.691 1.849 0.86 0.222 4.86 0.734 0.026 0.657 0.894 19.055 0.221 0.894 0.313 3.291 0.062 0.181 15.378 2.103 6.762 13.503 0.675 9.99 3.426 0.172 3.381 9.715 0.072 2.361 1.649 11.058 3.531 0.522 3.934 12.917 1.627 6.584 2.119 12.768 3.796 5.737 1.66 3.514 6.106 1.455 1.351 2.924 0.308 15.135 3.381 0.871 5.552 2.229 2.767 2.973 1.966 1.913 2.112 18.51 9.213 1.032 2.847 1.619 1.161 3.181 0.863 0.414 0.87 0.04 17.989 13.763 3.435 0.149 1.602 1.122 1.206 7.252 0.664 2.185 2.522 3.091 19.386 20.65 2.812 1.42 0.898 16.719 19.249 9.208 6.646 1.193 16.742 15.0 

SpectrumHMM Model: * M[0] - Mass:-537132.6 Overlap:4/5 LogOddsScore:8.115426445171428, SumScore:60.0, InsertsAfter: 1
 * M[1] - Mass:-259769.8 Overlap:3/5 LogOddsScore:3.2351722916053958, SumScore:35.127, InsertsAfter: 13
 * M[2] - Mass:-241034.62500000003 Overlap:3/5 LogOddsScore:5.6566571442724936, SumScore:51.586, InsertsAfter: 3
 * M[3] - Mass:-146642.6 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:40.513, InsertsAfter: 15
 * M[4] - Mass:-128032.42105263157 Overlap:5/5 LogOddsScore:9.363453319736813, SumScore:89.713, InsertsAfter: 3
 * M[5] - Mass:0.0 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:110.72800000000001, InsertsAfter: 48
 * M[6] - Mass:128079.55 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:149.93099999999998, InsertsAfter: 33
 * M[7] - Mass:215075.6 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:158.26500000000004, InsertsAfter: 20
 * M[8] - Mass:272054.45 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:133.366, InsertsAfter: 6
 * M[9] - Mass:343073.74999999994 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:163.32099999999997, InsertsAfter: 20
 * M[10] - Mass:472109.0 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:173.809, InsertsAfter: 36
 * M[11] - Mass:585253.3 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:195.956, InsertsAfter: 27
 * M[12] - Mass:716159.8500000001 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:175.353, InsertsAfter: 25
 * M[13] - Mass:844329.6500000001 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:182.215, InsertsAfter: 19
 * M[14] - Mass:941397.5833333333 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:128.351, InsertsAfter: 20
 * M[15] - Mass:998481.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:120.0, InsertsAfter: 12
ConsensusPRM: -537132 -259769 -241034 -146642 -128032 0 128079 215075 272054 343073 472109 585253 716159 844329 941397 998481 Consensus: -537132 -259769 -241034 -146642 -128032 0 128079 215075 272054 343073 472109 585253 716159 844329 941397 998481
De Novo: IQKSGAEIMKPG, Merged: IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGE
-537132 -259769 -241034 -146642 -128032 0 128079 215075 272054 343073 472109 585253 716159 844329 941397 998481 1069518 1156550 1255618 1383712 1496796 1583828 1743912 1872006 1943043 2044090 2101111 2264174 2365221 2512289 2613336 2670357 2833420 3019499 3132583 3261625 3447704 3546772 3674866 3802924 3959025 4056077 4113098 4250156 4307177 4420261 4549303 4735382 4848466 4905487 5034529 
60.0 35.127 51.586 40.513 89.713 70.364 112.46549999999999 124.13250000000002 111.683 126.66049999999998 139.40449999999998 150.478 140.1765 143.60750000000002 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 390.0 390.0 390.0 390.0 390.0 360.0 315.0 195.0 105.0 105.0 60.0 

(LEFT)Round: 1 for seed: IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGE
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_700_0.prm:24
 Score: 186.44400000000002, AlignedPeaks: 296091 409011 537082 665138 752152 809068 880145 1009180 1122217 1253256 1381336 
0 146572 163328 173826 275717 276499 277165 295179 296091 390195 409011 425965 426259 447333 447751 518197 519217 535954 537082 548090 551918 555002 561337 590298 608266 615782 647245 665138 677833 708576 711203 717292 717830 734245 752152 783564 809068 837912 847428 862299 880145 904072 951595 952013 969097 973087 973381 990364 992285 997531 1009180 1010371 1018416 1103290 1122217 1140154 1225208 1225520 1252774 1253256 1253545 1381336 
15.0 7.322 0.724 0.013 0.64 0.269 11.334 2.434 19.117 13.212 18.716 5.81 5.223 6.055 4.251 0.347 12.175 1.122 18.896 2.809 0.612 1.699 4.066 5.509 3.501 0.963 8.687 14.021 0.667 2.933 0.733 0.719 1.646 9.689 12.376 0.051 8.823 3.886 0.695 17.805 12.719 0.016 4.367 4.663 0.191 3.929 2.718 15.855 0.737 1.657 13.158 1.319 2.839 19.451 26.409 1.147 1.318 1.379 9.865 12.209 11.403 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1175_0.prm:29
 Score: 165.956, AlignedPeaks: 409142 537136 665243 752178 809101 880178 1009264 1122393 1253273 1381406 
0 326330 364134 380858 391617 408604 409142 410099 423561 425660 426994 428682 431026 444577 454150 472169 519301 537136 553889 559307 658084 662910 665243 713176 745340 749835 752178 809101 826262 873249 878012 880178 881436 963205 991242 1005511 1007181 1009264 1017302 1089139 1098566 1122393 1193382 1201475 1229444 1253273 1323709 1334543 1342621 1343373 1379311 1381406 1388640 1399414 1444124 1452945 1453668 1470409 1471644 1478511 1507558 1525583 1542760 1559507 1560736 1599721 1602010 1606514 1635588 1638669 1651827 1655626 1668929 1686669 1688935 1693529 1699357 1717422 1751551 1766636 1769608 1792561 1794774 1812528 1814758 1879676 1897695 1920819 1939491 1942703 1943177 1960228 1970987 1987711 2025515 
15.0 3.048 3.506 6.238 9.524 22.829 25.057 14.764 4.023 8.127 3.058 3.886 6.752 7.956 1.522 4.719 0.053 13.553 3.067 7.704 1.485 1.732 16.874 0.722 1.985 0.499 16.361 12.241 0.619 3.096 0.169 18.308 1.503 0.17 0.278 0.881 2.279 16.08 0.726 0.884 3.967 14.34 4.879 0.959 8.059 15.186 1.039 0.606 9.572 1.162 2.205 17.956 3.08 2.078 2.854 2.478 1.634 3.469 19.907 6.5 1.666 2.455 5.601 0.568 7.072 15.312 0.024 8.158 3.192 2.84 0.844 2.116 2.149 19.922 0.108 6.267 1.242 1.777 1.466 2.915 1.161 13.976 1.191 4.78 22.649 0.299 1.888 5.009 1.983 22.529 19.671 11.974 5.517 1.311 1.73 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:46
 Score: 164.06400000000002, AlignedPeaks: 312061 425044 553105 681212 768285 825479 896198 1025233 1138432 1269394 1397448 
0 127741 162640 174083 244880 263012 277103 278038 294170 310860 312061 315240 330985 332346 365214 402355 411205 425044 425507 429190 440812 441441 443043 459090 459710 460335 472220 478089 534841 535473 553105 554290 568294 568853 570717 588108 600215 681212 685330 703532 768285 807171 816333 816940 824739 825479 834478 844275 869461 886112 896198 929495 945740 947621 986217 994056 995054 1008997 1025233 1040138 1040844 1049306 1058499 1076693 1085276 1110462 1133297 1137797 1138432 1147566 1165609 1186467 1189690 1198221 1204525 1238454 1241579 1253187 1269394 1273543 1287383 1291544 1354521 1366629 1369568 1384020 1385884 1386443 1387663 1397448 1401595 1415411 1419264 1419896 1476648 1482516 1494381 1495646 1511694 1513296 1513925 1529230 1529693 1543531 1561704 1622391 1642638 1660608 1691725 1709857 1780654 1808865 1936726 
15.0 8.487 2.59 1.556 6.006 6.842 0.256 3.349 9.292 6.761 18.01 4.215 3.038 0.293 1.187 1.596 0.362 19.277 16.021 1.387 1.243 1.691 1.849 0.86 0.222 4.86 0.734 0.026 0.657 0.894 19.055 0.221 0.894 0.313 3.291 0.062 0.181 15.378 2.103 6.762 13.503 0.675 9.99 3.426 0.172 3.381 9.715 0.072 2.361 1.649 11.058 3.531 0.522 3.934 12.917 1.627 6.584 2.119 12.768 3.796 5.737 1.66 3.514 6.106 1.455 1.351 2.924 0.308 15.135 3.381 0.871 5.552 2.229 2.767 2.973 1.966 1.913 2.112 18.51 9.213 1.032 2.847 1.619 1.161 3.181 0.863 0.414 0.87 0.04 17.989 13.763 3.435 0.149 1.602 1.122 1.206 7.252 0.664 2.185 2.522 3.091 19.386 20.65 2.812 1.42 0.898 16.719 19.249 9.208 6.646 1.193 16.742 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_975_0.prm:3
 Score: 163.84599999999998, AlignedPeaks: 312090 425063 552914 680975 768160 825101 896101 1025166 1138165 1269164 1397188 
0 143697 162970 244982 262876 276282 277218 294157 296145 297457 310417 311079 311689 312090 322155 332242 347907 350307 365145 393091 407211 411239 420940 425063 429430 441897 442868 454134 458933 460388 534969 550942 552914 568953 570650 583395 678970 680975 681414 685379 700966 703232 721361 768160 816385 825101 834201 851252 896101 929379 945419 947356 985913 993963 994754 1025166 1039854 1040583 1058494 1076169 1132917 1138165 1147458 1186427 1189444 1198107 1204282 1238314 1241380 1253593 1255549 1269164 1273118 1273557 1275562 1287060 1291422 1369232 1371137 1395236 1397188 1400114 1401683 1403590 1415103 1419563 1433328 1482302 1494144 1495599 1512635 1529492 1543293 1547321 1622370 1642442 1642843 1660375 1674321 1691656 1709550 1773842 1808811 1936521 
15.0 0.223 7.465 6.987 4.485 0.739 0.48 0.958 2.004 2.388 6.63 7.433 15.814 17.331 10.8 4.504 0.589 2.591 1.631 0.29 0.168 0.826 3.45 21.301 1.972 5.94 0.615 0.67 2.692 0.316 0.143 1.236 19.828 1.954 3.058 2.968 0.828 15.922 15.428 1.452 2.35 9.312 0.406 10.822 11.156 3.48 13.202 1.304 10.749 4.678 1.531 2.499 10.382 3.041 5.314 12.07 3.465 4.696 6.638 1.644 3.318 17.442 2.506 4.902 3.057 2.517 2.324 1.824 1.013 6.662 0.143 19.254 9.678 11.578 0.029 1.201 2.243 1.809 0.065 0.558 15.647 0.572 16.381 0.562 3.395 1.153 0.808 0.179 2.769 0.369 0.439 22.618 1.331 1.127 7.234 14.262 11.883 9.886 1.358 6.714 11.294 2.12 15.048 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_700_0.prm:16
 Score: 163.65800000000002, AlignedPeaks: 296143 409180 537215 665259 752261 809148 880283 1009327 1122525 1253169 1381648 
0 277175 277729 296143 390255 392271 409180 424209 442051 450681 519267 532358 536559 537215 552315 555355 572386 590450 608585 615702 647352 665259 677217 686025 708829 711684 714260 717149 722441 734298 752261 809148 827189 847343 847959 861552 862380 879130 880283 894254 899589 904385 948977 975527 986224 990363 1004182 1007387 1009327 1010377 1013319 1018652 1027204 1035377 1068676 1103504 1121929 1122525 1253169 1381648 
15.0 14.501 9.016 14.459 17.777 0.741 14.89 5.702 0.352 1.036 11.058 0.552 1.788 19.891 0.904 2.438 3.851 10.216 4.199 0.059 7.189 12.611 0.098 1.529 1.998 1.847 3.311 1.101 1.017 9.682 9.829 8.096 2.856 1.157 2.422 0.616 18.16 1.332 12.087 0.801 3.108 0.583 0.098 8.507 0.391 10.147 1.99 2.432 12.051 0.75 0.384 1.928 1.822 0.334 0.534 14.403 5.16 19.376 10.368 15.0 

SpectrumHMM Model: * M[0] - Mass:-312075.5 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 0
 * M[1] - Mass:-296121.0 Overlap:3/5 LogOddsScore:5.6566571442724936, SumScore:45.0, InsertsAfter: 0
 * M[2] - Mass:-18735.8 Overlap:3/5 LogOddsScore:3.2351722916053958, SumScore:35.126999999999995, InsertsAfter: 18
 * M[3] - Mass:-1041.3333333333333 Overlap:3/5 LogOddsScore:2.0244298652718467, SumScore:16.628, InsertsAfter: 5
 * M[4] - Mass:0.0 Overlap:6/7 LogOddsScore:12.851380015760617, SumScore:120.50300000000001, InsertsAfter: 1
 * M[5] - Mass:112978.35294117648 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:188.95399999999995, InsertsAfter: 23
 * M[6] - Mass:240984.11764705883 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:161.587, InsertsAfter: 43
 * M[7] - Mass:369061.9411764706 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:187.27149999999997, InsertsAfter: 29
 * M[8] - Mass:456095.4705882353 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:187.0235, InsertsAfter: 24
 * M[9] - Mass:513066.88235294115 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:147.704, InsertsAfter: 6
 * M[10] - Mass:584070.5294117647 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:191.58149999999995, InsertsAfter: 18
 * M[11] - Mass:713123.9411764707 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:205.53149999999997, InsertsAfter: 36
 * M[12] - Mass:826229.705882353 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:243.18, InsertsAfter: 28
 * M[13] - Mass:957156.3529411764 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:215.7035, InsertsAfter: 25
 * M[14] - Mass:1085286.5882352942 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:225.1995, InsertsAfter: 24
ConsensusPRM: -312075 -296121 -18735 -1041 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286 Consensus: -312075 -296121 -18735 -1041 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286
De Novo: [312.075]IQKSGAEIMK, Merged: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGE
-312075 -296121 -18735 -1041 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286 1182354 1239438 1310475 1397507 1496575 1624669 1737753 1824785 1984869 2112963 2184000 2285047 2342068 2505131 2606178 2753246 2854293 2911314 3074377 3260456 3373540 3502582 3688661 3787729 3915823 4043881 4199982 4297034 4354055 4491113 4548134 4661218 4790260 4976339 5089423 5146444 5275486 
30.0 45.0 35.126999999999995 16.628 86.0445 139.33349999999996 115.9755 149.86849999999998 155.57800000000003 129.6935 159.12099999999998 172.46799999999996 196.829 177.94 184.4035 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 390.0 390.0 390.0 390.0 390.0 360.0 315.0 195.0 105.0 105.0 60.0 

(LEFT)Round: 2 for seed: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGE
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_975_0.prm:3
 Score: 178.199, AlignedPeaks: 0 312090 425063 552914 680975 768160 825101 896101 1025166 1138165 1269164 
0 143697 162970 244982 262876 276282 277218 294157 296145 297457 310417 311079 311689 312090 322155 332242 347907 350307 365145 393091 407211 411239 420940 425063 429430 441897 442868 454134 458933 460388 534969 550942 552914 568953 570650 583395 678970 680975 681414 685379 700966 703232 721361 768160 816385 825101 834201 851252 896101 929379 945419 947356 985913 993963 994754 1025166 1039854 1040583 1058494 1076169 1132917 1138165 1147458 1186427 1189444 1198107 1204282 1238314 1241380 1253593 1255549 1269164 1273118 1273557 1275562 1287060 1291422 1369232 1371137 1395236 1397188 1400114 1401683 1403590 1415103 1419563 1433328 1482302 1494144 1495599 1512635 1529492 1543293 1547321 1622370 1642442 1642843 1660375 1674321 1691656 1709550 1773842 1808811 1936521 
15.0 0.223 7.465 6.987 4.485 0.739 0.48 0.958 2.004 2.388 6.63 7.433 15.814 17.331 10.8 4.504 0.589 2.591 1.631 0.29 0.168 0.826 3.45 21.301 1.972 5.94 0.615 0.67 2.692 0.316 0.143 1.236 19.828 1.954 3.058 2.968 0.828 15.922 15.428 1.452 2.35 9.312 0.406 10.822 11.156 3.48 13.202 1.304 10.749 4.678 1.531 2.499 10.382 3.041 5.314 12.07 3.465 4.696 6.638 1.644 3.318 17.442 2.506 4.902 3.057 2.517 2.324 1.824 1.013 6.662 0.143 19.254 9.678 11.578 0.029 1.201 2.243 1.809 0.065 0.558 15.647 0.572 16.381 0.562 3.395 1.153 0.808 0.179 2.769 0.369 0.439 22.618 1.331 1.127 7.234 14.262 11.883 9.886 1.358 6.714 11.294 2.12 15.048 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:46
 Score: 176.075, AlignedPeaks: 0 312061 425044 553105 681212 768285 825479 896198 1025233 1138432 1269394 
0 127741 162640 174083 244880 263012 277103 278038 294170 310860 312061 315240 330985 332346 365214 402355 411205 425044 425507 429190 440812 441441 443043 459090 459710 460335 472220 478089 534841 535473 553105 554290 568294 568853 570717 588108 600215 681212 685330 703532 768285 807171 816333 816940 824739 825479 834478 844275 869461 886112 896198 929495 945740 947621 986217 994056 995054 1008997 1025233 1040138 1040844 1049306 1058499 1076693 1085276 1110462 1133297 1137797 1138432 1147566 1165609 1186467 1189690 1198221 1204525 1238454 1241579 1253187 1269394 1273543 1287383 1291544 1354521 1366629 1369568 1384020 1385884 1386443 1387663 1397448 1401595 1415411 1419264 1419896 1476648 1482516 1494381 1495646 1511694 1513296 1513925 1529230 1529693 1543531 1561704 1622391 1642638 1660608 1691725 1709857 1780654 1808865 1936726 
15.0 8.487 2.59 1.556 6.006 6.842 0.256 3.349 9.292 6.761 18.01 4.215 3.038 0.293 1.187 1.596 0.362 19.277 16.021 1.387 1.243 1.691 1.849 0.86 0.222 4.86 0.734 0.026 0.657 0.894 19.055 0.221 0.894 0.313 3.291 0.062 0.181 15.378 2.103 6.762 13.503 0.675 9.99 3.426 0.172 3.381 9.715 0.072 2.361 1.649 11.058 3.531 0.522 3.934 12.917 1.627 6.584 2.119 12.768 3.796 5.737 1.66 3.514 6.106 1.455 1.351 2.924 0.308 15.135 3.381 0.871 5.552 2.229 2.767 2.973 1.966 1.913 2.112 18.51 9.213 1.032 2.847 1.619 1.161 3.181 0.863 0.414 0.87 0.04 17.989 13.763 3.435 0.149 1.602 1.122 1.206 7.252 0.664 2.185 2.522 3.091 19.386 20.65 2.812 1.42 0.898 16.719 19.249 9.208 6.646 1.193 16.742 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_975_0.prm:6
 Score: 152.264, AlignedPeaks: 0 312105 425185 553229 681290 768323 825320 896388 1025419 1138506 1269543 
0 255534 294093 297119 312105 332205 399175 410286 425185 429219 460261 535236 553229 570259 585278 681290 685407 703392 737840 768323 807348 816446 825320 827428 834427 844371 896388 929530 945479 947512 985969 986462 994972 995468 1009464 1025419 1040464 1040971 1058563 1076551 1127515 1133513 1138506 1147595 1165607 1186628 1190054 1198566 1204616 1241604 1269543 1273664 1287544 1291651 1369665 1384684 1396627 1397628 1401726 1415639 1419707 1494682 1529767 1543736 1561687 1589736 1622738 1642838 1657824 1660850 1700860 1808845 1936933 
15.0 2.203 0.299 0.893 10.552 0.105 3.152 6.151 11.767 1.0 0.498 0.072 14.502 3.858 0.121 12.654 3.221 5.346 0.807 12.688 0.245 11.861 5.003 1.526 8.761 0.049 10.517 3.464 1.412 2.466 1.798 11.495 3.311 5.247 1.362 10.161 2.586 2.981 8.735 2.137 0.065 2.505 16.691 3.085 1.06 5.847 1.703 2.999 4.416 1.879 17.729 8.957 2.287 3.327 2.768 0.124 3.116 9.889 12.04 3.724 3.907 1.531 14.983 0.512 0.26 1.355 2.637 6.212 1.712 2.557 2.887 6.146 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:48
 Score: 124.21599999999998, AlignedPeaks: 0 312494 425071 552964 681017 768408 825077 896085 1025037 1138084 1269133 
0 144489 162637 242935 262698 291097 294456 296325 308205 311504 312494 349918 353301 393361 409112 411219 420900 425071 426908 439843 441762 455980 459773 460532 517985 522202 551748 552964 567381 568844 570695 583601 584981 600344 681017 681669 682925 685396 700763 702150 703372 715084 767918 768408 793386 811611 816452 822430 825077 834474 845306 895287 896085 909869 929545 947445 984998 985891 994759 995469 1008611 1025037 1040324 1109230 1128205 1132106 1132820 1138084 1147466 1161150 1186128 1186618 1204340 1221357 1241203 1252386 1253147 1253744 1261967 1269133 1271611 1272867 1273506 1286092 1354192 1369555 1370935 1380342 1382777 1383841 1385692 1387155 1395208 1397202 1401572 1402788 1415222 1419355 1432334 1436551 1494763 1498532 1512774 1514693 1529449 1543317 1545424 1547862 1642042 1643032 1658211 1691838 1711601 1792559 1808650 1936526 
15.0 2.689 0.748 2.297 2.659 0.806 0.304 4.042 3.329 7.968 2.772 3.418 0.603 0.314 1.81 1.823 4.265 11.134 2.413 5.78 2.925 3.605 6.492 2.597 1.542 0.021 10.117 8.371 2.106 2.673 1.892 2.697 0.574 1.294 7.382 1.577 1.361 2.547 1.843 5.387 12.319 1.422 11.897 11.897 1.213 1.018 10.43 0.709 2.688 8.377 0.624 3.216 6.356 2.654 6.056 2.131 3.862 14.585 4.952 1.95 1.18 10.624 4.852 1.875 1.876 1.084 2.176 13.683 3.412 0.488 8.297 8.435 4.653 2.041 1.94 0.301 6.459 5.813 1.7 19.309 0.211 0.236 5.698 2.653 1.95 2.504 1.436 0.322 1.27 0.238 0.873 2.334 2.453 12.292 3.309 1.833 5.774 5.109 1.591 0.924 0.882 5.985 2.932 1.375 15.668 0.021 2.793 0.703 2.032 1.635 0.011 2.478 1.847 6.173 12.012 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_975_0.prm:39
 Score: 115.305, AlignedPeaks: 0 312104 425187 553227 681289 768311 896362 1025416 1138503 1269531 
0 281373 302295 312104 335280 376286 387576 425187 468297 513386 520333 549445 553227 566302 570227 681289 703408 768311 807338 816447 834423 896362 929532 947541 986460 995463 1025416 1040468 1076552 1133504 1138503 1147603 1186640 1198548 1204618 1240610 1269531 1273660 1291629 1311272 1384714 1388639 1397625 1401714 1415633 1529754 1572494 1578655 1619661 1642837 1652646 1673568 1936931 
15.0 2.446 3.787 7.139 0.397 4.15 2.553 0.079 1.143 2.854 3.301 1.482 8.246 0.158 0.275 11.518 6.439 12.804 0.288 11.425 8.943 7.504 2.826 2.518 10.586 3.78 10.134 3.013 2.937 1.516 16.994 1.177 4.612 2.27 3.546 2.083 10.887 7.581 3.327 1.678 0.454 2.023 9.991 2.845 0.36 3.763 0.245 0.894 1.507 4.963 5.033 2.292 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:105.0, InsertsAfter: 0
 * M[1] - Mass:162749.0 Overlap:3/7 LogOddsScore:1.3365695619021236, SumScore:10.802999999999999, InsertsAfter: 3
 * M[2] - Mass:244931.0 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:12.993, InsertsAfter: 2
 * M[3] - Mass:262862.0 Overlap:3/7 LogOddsScore:1.3365695619021236, SumScore:13.986, InsertsAfter: 1
 * M[4] - Mass:311076.4 Overlap:3/7 LogOddsScore:1.3365695619021236, SumScore:22.162, InsertsAfter: 17
 * M[5] - Mass:312139.06666666677 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:141.8485, InsertsAfter: 1
 * M[6] - Mass:425091.0 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:202.89149999999995, InsertsAfter: 27
 * M[7] - Mass:553065.1333333333 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:185.97750000000002, InsertsAfter: 36
 * M[8] - Mass:681138.4666666668 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:212.7225, InsertsAfter: 20
 * M[9] - Mass:768269.7333333333 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:217.292, InsertsAfter: 19
 * M[10] - Mass:825255.357142857 Overlap:6/7 LogOddsScore:8.00841031042642, SumScore:144.2455, InsertsAfter: 13
 * M[11] - Mass:896202.4666666668 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:205.30499999999995, InsertsAfter: 13
 * M[12] - Mass:1025236.0666666665 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:228.22499999999997, InsertsAfter: 33
 * M[13] - Mass:1138325.3999999997 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:276.774, InsertsAfter: 28
 * M[14] - Mass:1269325.9333333333 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:263.629, InsertsAfter: 41
ConsensusPRM: 0 162749 244931 262862 311076 312139 425091 553065 681138 768269 825255 896202 1025236 1138325 1269325 Consensus: 0 162749 244931 262862 311076 312139 425091 553065 681138 768269 825255 896202 1025236 1138325 1269325
De Novo: [312.139]IQQSGAEIM, Merged: [312.139]IQQSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGE
0 162749 244931 262862 311076 312139 425091 553065 681138 768269 825255 896202 1025236 1138325 1269325 1397455 1494523 1551607 1622644 1709676 1808744 1936838 2049922 2136954 2297038 2425132 2496169 2597216 2654237 2817300 2918347 3065415 3166462 3223483 3386546 3572625 3685709 3814751 4000830 4099898 4227992 4356050 4512151 4609203 4666224 4803282 4860303 4973387 5102429 5288508 5401592 5458613 5587655 
67.5 10.802999999999999 12.993 13.986 22.162 113.9465 171.11249999999995 150.97650000000002 181.2955 186.435 136.96949999999998 182.21299999999997 200.34649999999996 236.8015 220.7845 184.4035 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 390.0 390.0 390.0 390.0 390.0 360.0 315.0 195.0 105.0 105.0 60.0 
(RIGHT)Round: 0 for seed: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGE
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1350_0.prm:2
 Score: 154.499, AlignedPeaks: 0 154563 291509 461367 590266 776313 889309 946379 1075412 
0 154563 291509 293097 326909 329034 362913 383005 404286 422283 425066 433333 436245 443033 458250 460953 461367 533227 544387 551302 553117 562180 572302 577305 589081 590266 598360 645307 648230 665310 707314 735464 748363 752480 774644 776313 792015 794086 828282 861411 887187 889309 907162 925129 942440 946379 960191 963881 984397 1034432 1043398 1073351 1075412 1091355 1130430 1160493 1186292 1187479 1188500 1204403 1205447 1206320 1274714 1275472 1288293 1291418 1331387 1334002 1369267 1369989 1372604 1378545 1415698 1424567 1428513 1429277 1497615 1498544 1515536 1516513 1543498 1573637 1612636 1628610 1646536 1660640 1668475 1669559 1697746 1719594 1743800 1757672 1761589 1778812 1796830 1814717 1842580 1927748 1945579 1955628 1968527 1996677 2038681 2055762 2058685 2105632 2113725 2131689 2170764 2242625 2260716 2278926 2281708 2299706 
15.0 4.046 6.971 4.391 7.495 2.646 2.191 2.394 4.306 8.229 1.719 4.413 4.081 8.737 5.257 16.345 16.345 4.279 3.356 11.032 9.342 4.847 6.192 2.629 6.08 12.735 5.376 4.087 3.654 7.916 3.23 0.767 1.435 0.942 0.803 20.429 0.411 0.268 2.831 0.323 0.461 25.302 2.929 8.694 9.447 16.963 2.079 0.334 0.23 0.358 4.959 1.227 21.708 0.668 6.526 1.21 3.042 13.742 17.269 1.868 5.673 13.105 13.393 20.854 0.828 1.034 0.423 0.134 3.685 1.912 7.185 2.145 2.282 2.082 19.887 3.04 4.154 0.084 16.855 2.782 1.599 5.91 1.249 20.582 1.917 7.366 0.988 1.983 1.058 1.405 1.36 15.612 10.754 3.067 1.47 21.179 2.121 6.962 1.842 2.55 0.293 1.414 4.701 1.702 1.759 0.198 2.134 1.984 6.643 1.202 2.252 4.46 4.01 1.204 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:173
 Score: 114.925, AlignedPeaks: 0 153697 291159 348157 461154 590297 776205 889342 1075374 
0 130764 153697 273185 274585 275420 289249 291159 292785 293278 305263 309541 311345 345669 347261 348157 348721 404207 406351 420621 422197 439333 443255 459565 461154 517702 537877 552361 572266 575381 589019 590297 592600 594475 605258 640043 648946 714324 715009 717307 725587 752470 759102 769123 776205 781801 797554 804019 825592 827031 840921 864735 876721 879946 883206 886724 889342 891357 903481 909380 911393 922532 967332 975145 1016300 1030670 1033310 1039327 1043366 1057299 1061580 1063482 1067921 1068557 1074374 1075374 1082380 1097609 1132524 1133282 1182370 1186563 1188696 1189434 1190230 1205628 1207392 1208294 1210430 1216672 1217882 1273694 1275591 1290301 1292666 1293883 1295701 1297669 1315676 1319800 1406329 1410453 1428481 1430428 1432246 1433463 1435832 1446540 1450541 1508247 1509457 1515709 1517835 1518737 1535899 1536695 1537453 1543759 1592847 1593605 1628520 1643749 1650755 1651755 1657567 1658208 1662647 1664549 1668830 1682763 1686802 1692818 1695459 1709829 1750984 1758797 1803597 1828730 1834772 1836792 1839405 1842923 1846187 1849408 1860700 1861394 1867889 1868524 1874433 1885208 1899098 1900537 1922110 1949924 1957006 1967027 1968332 1973024 1973659 2000542 2008822 2011120 2011805 2077183 2086085 2120871 2131655 2133530 2135839 2153864 2188252 2208427 2265024 2292542 2303932 2319779 2321922 2351860 2377972 2414784 2416588 2432851 2433344 2434970 2435764 2436880 2450709 2452944 2455129 2595364 2708119 
15.0 3.613 6.812 3.311 4.323 2.1 1.476 16.119 15.37 14.676 0.784 5.424 6.001 2.995 2.452 8.769 2.791 1.152 2.463 1.946 4.006 0.167 2.378 2.528 15.49 1.273 1.46 1.231 2.592 4.097 2.895 13.075 1.33 2.001 1.434 6.549 3.103 5.528 3.761 1.903 3.22 0.577 0.56 0.359 10.191 0.837 0.285 0.64 0.548 1.857 1.468 0.023 2.926 0.748 3.99 5.004 3.446 2.101 2.52 2.448 0.753 5.944 0.636 2.571 1.758 2.916 1.798 0.759 0.723 2.433 1.96 1.37 3.538 5.664 4.864 11.023 0.715 2.329 2.128 1.557 3.389 1.742 11.733 0.887 1.859 0.377 3.245 5.804 9.794 0.188 3.342 0.146 13.621 3.515 2.293 3.061 4.84 17.267 3.54 0.602 0.541 0.655 16.565 4.023 0.674 3.259 5.002 9.388 13.924 3.856 1.189 11.487 5.074 3.387 1.454 4.442 14.339 3.566 3.586 2.615 0.944 0.459 8.607 4.376 7.979 4.656 0.706 0.218 1.836 0.066 0.74 0.79 1.509 2.7 3.378 1.488 8.669 2.398 3.92 5.94 6.515 2.899 5.968 1.983 7.332 6.702 2.144 4.232 2.052 0.682 1.53 1.521 1.317 7.936 2.441 2.58 3.503 2.836 0.675 4.823 2.533 3.763 3.832 3.972 6.237 0.786 1.509 0.562 10.298 8.022 0.478 0.485 11.64 0.577 4.038 1.15 1.828 0.606 6.489 0.602 0.143 13.646 12.296 11.302 3.545 1.152 1.209 3.858 1.142 2.282 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:274
 Score: 114.48, AlignedPeaks: 0 291230 348432 461157 590250 776329 889284 946260 1075418 
0 131031 141857 162651 202341 273177 289150 290655 291230 315224 331051 331746 338241 339194 347853 348432 374051 385512 415420 433356 443302 459728 460205 461157 478374 512082 523988 537850 548561 571644 589612 590250 607333 614310 629362 634619 637671 657831 686426 729780 735359 736248 758491 776329 789069 798096 807061 807909 850537 889284 905089 906709 907515 934137 945375 946260 949355 952001 979334 1000052 1032684 1056690 1067711 1073319 1075418 1091187 1092470 1149764 1170301 1186266 1188514 1205375 1214041 1214704 1257556 1270655 1273512 1275477 1290971 1291730 1293445 1299254 1315694 1363256 1371930 1372372 1373653 1379066 1391691 1401780 1428733 1429541 1459622 1487383 1497472 1515510 1516791 1517233 1525907 1573622 1589909 1595718 1598192 1613663 1615651 1631607 1674459 1675122 1683776 1700698 1702897 1739399 1748304 1761891 1796693 1797976 1813747 1815844 1821452 1832473 1853747 1856479 1889111 1909829 1937162 1939808 1943788 1954312 1977158 1981648 1982454 1984074 1999879 2038626 2081254 2082101 2091067 2100094 2112834 2130672 2152915 2153804 2159383 2202737 2231332 2251492 2259802 2267565 2274853 2281759 2298913 2299535 2317519 2351313 2365176 2410756 2428054 2428958 2429416 2452721 2455807 2473743 2503651 2540731 2549969 2557417 2558112 2573939 2590035 2597933 2598508 2600013 2608825 2615986 2686822 2758132 2871153 
15.0 2.079 2.729 2.197 1.936 2.428 4.309 2.699 12.44 2.147 3.826 2.818 3.85 10.43 2.034 9.848 1.941 0.581 2.4 1.59 3.49 7.606 11.22 15.467 14.372 0.615 1.922 2.322 1.264 1.945 12.114 13.093 14.986 2.321 2.815 1.631 1.252 2.61 4.078 2.079 4.149 4.977 2.19 9.844 1.49 3.15 3.137 2.693 0.848 9.406 0.945 1.037 2.917 0.209 1.879 1.075 0.849 0.41 1.735 0.477 0.124 1.734 1.782 4.325 13.307 1.828 3.424 2.608 2.026 1.882 14.647 5.252 1.621 0.701 1.801 0.945 6.145 22.926 4.252 4.87 10.291 2.843 7.554 2.657 16.074 14.853 4.213 0.95 3.016 1.341 4.128 6.625 5.9 1.567 2.185 7.91 14.583 16.39 2.18 10.141 3.325 5.108 2.833 25.487 5.464 7.833 4.804 3.509 6.057 13.032 0.242 5.579 0.212 0.026 3.287 3.232 15.864 4.827 1.76 6.582 0.785 0.343 4.451 0.595 0.261 0.417 3.156 1.043 2.651 2.913 1.785 1.118 8.422 4.039 2.825 5.538 4.182 1.167 7.229 6.166 4.256 4.041 2.085 4.152 3.508 1.981 0.631 0.586 2.105 11.042 16.336 7.14 5.898 1.948 0.827 8.734 10.982 4.728 4.076 0.281 0.845 0.745 0.29 4.136 3.319 0.585 1.047 1.0 0.787 9.727 0.159 3.296 1.108 4.632 2.13 2.311 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:870
 Score: 110.161, AlignedPeaks: 348147 461194 590213 776302 889337 946426 1075292 
0 146877 171212 203997 232082 317018 332964 348147 446041 459208 461194 495061 503116 521000 555669 590213 619992 632152 634095 647262 648026 648650 662458 663392 671374 676726 705018 707031 745175 748602 774208 776302 778119 794260 889337 907145 946426 1075292 
15.0 10.853 1.479 23.001 2.193 22.143 3.231 5.245 1.993 0.733 13.458 2.27 10.693 2.206 0.915 4.668 3.857 13.415 2.332 0.114 0.583 3.183 3.826 1.461 0.178 1.764 3.13 0.998 6.574 1.25 1.18 12.238 0.409 3.028 20.655 3.186 8.897 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:516
 Score: 104.47500000000001, AlignedPeaks: 284274 438383 575522 632332 745342 874431 1060459 1173501 1359652 
0 157996 162898 204115 284274 316259 317180 334256 391776 438383 503193 520248 521200 558220 575522 622551 632332 649377 673016 696768 697538 706228 745342 762182 762803 770264 770924 790730 798855 799459 802195 804905 813286 819442 846798 847470 855837 861232 869969 874431 939279 940374 948785 949666 956460 965761 1016613 1027266 1028647 1043406 1060459 1061403 1093374 1173501 1359652 
15.0 0.043 1.767 13.945 18.553 2.438 25.454 13.171 0.094 0.546 14.437 6.525 0.574 0.476 6.346 1.166 8.894 3.951 0.546 1.901 8.454 3.621 5.235 3.149 0.796 0.7 2.548 4.87 2.383 4.757 4.549 0.317 1.974 2.081 1.074 4.591 3.401 0.06 1.718 11.861 0.031 0.827 0.692 0.754 0.05 1.373 1.262 0.282 1.552 0.033 11.941 2.099 18.347 11.099 15.0 

SpectrumHMM Model: * M[0] - Mass:0.75 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:468.553, InsertsAfter: 3
 * M[1] - Mass:97052.0 Overlap:2/7 LogOddsScore:3.0163028121648807, SumScore:390.0, InsertsAfter: 5
 * M[2] - Mass:154122.38461538462 Overlap:5/7 LogOddsScore:6.760383435861036, SumScore:401.404, InsertsAfter: 16
 * M[3] - Mass:291287.47058823524 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:431.87600000000003, InsertsAfter: 19
 * M[4] - Mass:348215.8 Overlap:6/7 LogOddsScore:8.00841031042642, SumScore:422.75600000000003, InsertsAfter: 32
 * M[5] - Mass:461210.0999999999 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:425.99500000000006, InsertsAfter: 41
 * M[6] - Mass:590253.0499999998 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:370.432, InsertsAfter: 57
 * M[7] - Mass:776277.7 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:259.643, InsertsAfter: 25
 * M[8] - Mass:889315.6 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:174.908, InsertsAfter: 14
 * M[9] - Mass:946360.7692307692 Overlap:5/7 LogOddsScore:7.971125862194585, SumScore:131.935, InsertsAfter: 27
 * M[10] - Mass:1075387.65 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:136.038, InsertsAfter: 16
 * M[11] - Mass:1188570.0 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:43.649, InsertsAfter: 4
 * M[12] - Mass:1205628.8333333333 Overlap:3/3 LogOddsScore:3.923032594975119, SumScore:18.734, InsertsAfter: 12
 * M[13] - Mass:1275513.3333333335 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:57.400999999999996, InsertsAfter: 20
 * M[14] - Mass:1372488.0 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:22.038, InsertsAfter: 9
 * M[15] - Mass:1428564.4285714284 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:40.58, InsertsAfter: 16
 * M[16] - Mass:1515905.2499999998 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:42.925, InsertsAfter: 10
 * M[17] - Mass:1573629.5 Overlap:2/3 LogOddsScore:1.464263294076185, SumScore:16.051000000000002, InsertsAfter: 8
 * M[18] - Mass:1628565.0 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:21.526, InsertsAfter: 124
 * M[19] - Mass:2281733.5 Overlap:2/3 LogOddsScore:1.464263294076185, SumScore:15.052, InsertsAfter: 46
ConsensusPRM: 0 97052 154122 291287 348215 461210 590253 776277 889315 946360 1075387 1188570 1205628 1275513 1372488 1428564 1515905 1573629 1628565 2281733 Consensus: 0 97052 154122 291287 348215 461210 590253 776277 889315 946360 1075387 1188570 1205628 1275513 1372488 1428564 1515905 1573629 1628565 2281733
De Novo: PGHGIEWIGEISP[256.077], Merged: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISP[256.077]
-312075 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286 1182354 1239438 1310475 1397507 1496575 1624669 1737753 1824785 1984869 2112963 2184000 2285047 2342068 2505131 2606178 2753246 2854293 2911314 3074377 3260456 3373540 3502582 3688661 3787729 3915823 4043881 4199982 4297034 4354055 4491113 4548134 4661218 4790260 4976339 5089423 5146444 5275486 5388669 5405727 5475612 5572587 5628663 5716004 5773728 5828664 6481832 
30.0 86.0445 139.33349999999996 115.9755 149.86849999999998 155.57800000000003 129.6935 159.12099999999998 172.46799999999996 196.829 177.94 184.4035 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 429.2765 381.65783436474646 392.36513374589856 409.2695668729493 404.70956687294927 392.99750000000006 342.716 227.3215 139.954 115.13063374589859 98.019 43.649 18.734 57.400999999999996 18.70113374589859 40.58 42.925 12.714133745898593 18.18913374589859 11.71513374589859 
(RIGHT)Round: 1 for seed: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISP[256.077]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1350_0.prm:2
 Score: 179.372, AlignedPeaks: 461367 590266 776313 889309 946379 1075412 1188500 1275472 1372604 1628610 
0 154563 291509 293097 326909 329034 362913 383005 404286 422283 425066 433333 436245 443033 458250 460953 461367 533227 544387 551302 553117 562180 572302 577305 589081 590266 598360 645307 648230 665310 707314 735464 748363 752480 774644 776313 792015 794086 828282 861411 887187 889309 907162 925129 942440 946379 960191 963881 984397 1034432 1043398 1073351 1075412 1091355 1130430 1160493 1186292 1187479 1188500 1204403 1205447 1206320 1274714 1275472 1288293 1291418 1331387 1334002 1369267 1369989 1372604 1378545 1415698 1424567 1428513 1429277 1497615 1498544 1515536 1516513 1543498 1573637 1612636 1628610 1646536 1660640 1668475 1669559 1697746 1719594 1743800 1757672 1761589 1778812 1796830 1814717 1842580 1927748 1945579 1955628 1968527 1996677 2038681 2055762 2058685 2105632 2113725 2131689 2170764 2242625 2260716 2278926 2281708 2299706 
15.0 4.046 6.971 4.391 7.495 2.646 2.191 2.394 4.306 8.229 1.719 4.413 4.081 8.737 5.257 16.345 16.345 4.279 3.356 11.032 9.342 4.847 6.192 2.629 6.08 12.735 5.376 4.087 3.654 7.916 3.23 0.767 1.435 0.942 0.803 20.429 0.411 0.268 2.831 0.323 0.461 25.302 2.929 8.694 9.447 16.963 2.079 0.334 0.23 0.358 4.959 1.227 21.708 0.668 6.526 1.21 3.042 13.742 17.269 1.868 5.673 13.105 13.393 20.854 0.828 1.034 0.423 0.134 3.685 1.912 7.185 2.145 2.282 2.082 19.887 3.04 4.154 0.084 16.855 2.782 1.599 5.91 1.249 20.582 1.917 7.366 0.988 1.983 1.058 1.405 1.36 15.612 10.754 3.067 1.47 21.179 2.121 6.962 1.842 2.55 0.293 1.414 4.701 1.702 1.759 0.198 2.134 1.984 6.643 1.202 2.252 4.46 4.01 1.204 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_750_0.prm:85
 Score: 151.03300000000002, AlignedPeaks: 0 185667 298852 356212 484964 598205 685354 782515 
0 184163 185667 226254 298852 339125 356212 412040 468106 484964 485377 554227 570289 580642 581126 596850 598205 667066 668163 683394 684698 685354 687862 702333 703009 748885 758270 776580 782515 798180 800490 807049 816465 838449 849374 849909 888578 911410 928246 929558 962573 991170 1000131 1012772 1013416 1030654 1048745 1056716 1057468 1068666 1070705 1074620 1125930 1128444 1135451 1163649 1170656 1173170 1231733 1241632 1242384 1268446 1285684 1286328 1297392 1298969 1307930 1336526 1369542 1370854 1387690 1391548 1410522 1448077 1448524 1449725 1491085 1492051 1500920 1516585 1540829 1550215 1581284 1596091 1596767 1613752 1614402 1615706 1630937 1632034 1642158 1700893 1702250 1717707 1717974 1718458 1718808 1728811 1744873 1745891 1813762 1814226 1830994 1837776 1841933 1858891 1887060 1942865 1959974 2000258 2027898 2044937 2072846 2113432 2123344 2281089 
15.0 2.58 3.765 2.087 28.139 0.571 11.831 0.565 0.181 25.113 24.622 0.992 2.143 1.423 1.626 3.297 20.423 2.197 2.192 4.781 12.345 23.028 1.138 5.183 5.575 0.186 2.143 1.285 8.734 0.927 2.95 0.883 1.53 0.109 1.489 0.686 0.97 5.777 6.53 3.855 7.482 0.778 1.062 6.565 5.868 5.976 0.825 0.96 1.58 0.98 1.352 0.698 2.248 0.82 4.837 3.166 0.305 0.56 0.173 1.844 2.207 4.024 4.645 3.737 0.277 3.169 1.388 6.914 2.776 1.588 7.93 1.485 0.171 0.473 1.925 1.331 0.984 3.225 2.199 4.043 3.012 0.57 0.783 1.728 0.657 19.229 4.881 3.189 8.94 9.785 1.02 20.9 1.914 4.127 2.864 6.616 4.386 3.298 1.201 2.306 14.112 14.826 5.425 0.361 1.191 4.525 0.882 9.705 2.514 11.303 7.453 7.32 1.001 2.316 1.812 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:105
 Score: 131.113, AlignedPeaks: 0 299066 356324 485190 598253 685293 782248 
0 219903 230717 238531 239231 299066 310928 316864 323062 337178 339106 348101 350029 356324 366100 367361 368110 374380 386082 425069 441246 457252 479228 485190 485774 495261 497146 502809 570154 596018 598253 608235 616227 640153 657094 685293 703415 723281 741359 759271 760514 780335 782248 839283 857361 869351 878570 886328 897777 903524 908202 922427 925243 926558 948602 983339 1000386 1012066 1052454 1059431 1067251 1069807 1073859 1097967 1102019 1103290 1103931 1104575 1112395 1119378 1171433 1188372 1235250 1244292 1245268 1246483 1263624 1285510 1293256 1328367 1332543 1337573 1384776 1389578 1391491 1428294 1448538 1486515 1514732 1531673 1563562 1573556 1601672 1617664 1618628 1669017 1669716 1674680 1676565 1686660 1692568 1714574 1749919 1785684 1803717 1804465 1815586 1821842 1832720 1848764 1860898 1872760 1933295 1941109 1951923 1968768 2153816 
15.0 2.808 1.655 2.603 2.628 12.9 1.965 4.268 0.784 0.387 2.958 4.598 17.123 17.904 4.772 1.969 12.158 3.396 8.44 0.547 1.805 3.91 15.235 22.023 11.898 1.742 0.801 1.504 0.948 1.04 18.73 11.027 3.144 0.16 0.69 21.643 0.839 11.597 1.903 2.556 2.839 2.927 7.913 2.24 3.132 0.523 0.301 10.979 0.695 0.057 0.198 0.281 7.646 12.35 1.328 12.997 9.38 1.001 3.629 0.901 0.346 1.503 0.411 0.229 0.523 10.608 3.068 1.128 1.053 1.644 10.156 9.855 6.531 3.204 3.197 3.223 2.023 11.807 1.241 1.226 1.062 1.197 3.407 0.504 0.194 7.416 16.228 3.936 0.578 0.603 11.623 8.662 2.445 3.156 2.478 1.512 1.074 1.339 1.346 22.149 16.137 0.091 1.083 4.178 10.344 7.748 9.82 17.389 1.964 1.389 0.305 17.458 2.322 1.669 3.627 8.995 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:102
 Score: 128.89499999999998, AlignedPeaks: 0 299048 356034 485171 598264 685282 782406 
0 203625 220171 239097 299048 304368 309167 311092 323243 327206 339284 349629 350218 354815 355237 356034 365992 367393 368119 385690 386201 440211 457214 479215 485171 495186 497309 553477 570210 572081 598264 608267 614334 616312 685282 703173 722272 743490 760263 777990 778603 779373 782406 839161 839417 885333 885697 907296 926451 948501 965466 983438 999382 1035366 1039318 1058704 1070373 1100467 1103028 1118471 1131522 1171424 1187407 1205374 1222339 1234688 1244437 1285555 1327707 1331645 1384298 1388452 1392850 1427774 1428057 1448549 1485552 1513564 1562555 1572565 1598759 1600630 1616731 1617363 1668550 1673531 1673820 1675654 1685665 1691637 1730629 1758788 1802705 1803447 1820630 1831556 1871792 1950669 1951531 1951954 1967215 1967836 2152830 
15.0 5.069 3.65 4.787 12.287 0.344 0.457 1.148 0.43 4.245 2.637 7.578 16.307 4.221 4.128 8.064 6.909 1.912 14.388 4.147 2.233 1.584 5.18 15.332 25.784 0.544 0.087 0.007 0.824 2.291 20.273 3.713 0.154 1.288 23.948 0.385 8.447 0.091 3.992 0.097 5.615 5.015 8.539 6.087 4.39 4.047 3.33 2.004 16.455 0.875 0.254 15.254 7.262 2.643 1.188 2.341 1.275 0.546 10.731 1.0 0.856 11.285 7.18 0.966 0.783 8.14 12.906 7.259 0.4 3.553 4.157 2.393 0.271 1.823 2.676 10.095 4.753 1.084 5.39 7.081 1.101 3.753 4.94 1.031 0.571 1.685 1.635 1.063 19.358 14.35 0.271 1.31 9.884 4.348 17.661 0.902 12.419 6.256 1.083 1.96 2.006 11.478 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1050_0.prm:16
 Score: 128.424, AlignedPeaks: 0 298941 356078 485106 598122 685184 782276 
0 144132 185507 293065 297212 298941 299632 309065 310986 315895 316668 323180 327855 341339 351201 356078 368108 422144 425367 439152 440148 445199 454267 457094 485106 551310 570184 572187 596063 598122 598685 616170 665298 683143 685184 701060 703280 705560 721269 782276 813181 814258 827465 828365 839317 907031 926309 942318 960180 960871 964489 978375 983281 1030406 1033180 1040690 1043357 1047961 1065757 1070361 1074144 1074807 1130486 1152848 1171432 1187441 1206186 1215129 1274406 1285398 1286254 1299460 1300537 1331458 1355165 1355909 1399167 1428532 1448458 1456457 1515625 1541531 1543534 1559548 1560467 1562479 1610694 1628639 1630860 1656619 1673616 1674567 1691619 1701571 1745610 1790538 1802783 1814086 1814793 1820656 1939383 1951894 1967739 2095708 
15.0 0.888 2.998 10.849 3.827 16.901 9.751 3.195 10.204 4.219 5.045 1.891 3.613 5.196 0.954 5.173 1.752 16.383 0.649 4.774 8.589 2.049 0.979 13.92 20.654 3.852 0.934 1.965 1.465 18.081 7.289 2.086 4.972 0.409 24.346 1.366 4.235 0.208 0.884 13.269 2.18 0.836 0.218 8.415 10.472 1.712 16.222 9.608 1.157 0.244 0.557 1.171 9.737 0.715 0.917 0.294 0.513 1.345 0.364 3.159 11.368 6.977 2.923 0.648 10.408 9.041 11.55 2.292 6.441 12.864 0.747 2.57 1.342 3.229 2.111 2.997 6.205 2.603 12.031 2.792 6.732 1.895 4.418 4.807 2.717 6.569 0.738 13.826 0.49 5.508 17.457 1.139 14.005 0.15 0.397 1.959 10.872 2.154 22.102 10.405 2.935 3.376 19.065 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:404.70956687294927, InsertsAfter: 10
 * M[1] - Mass:113084.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:409.3425000000001, InsertsAfter: 8
 * M[2] - Mass:242090.25 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:415.451, InsertsAfter: 11
 * M[3] - Mass:427891.23076923075 Overlap:5/7 LogOddsScore:7.971125862194585, SumScore:254.51349999999996, InsertsAfter: 15
 * M[4] - Mass:541086.65 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:235.48300000000003, InsertsAfter: 30
 * M[5] - Mass:598258.4 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:175.06563374589857, InsertsAfter: 33
 * M[6] - Mass:727203.2999999998 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:213.301, InsertsAfter: 26
 * M[7] - Mass:840322.8500000001 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:138.42499999999998, InsertsAfter: 19
 * M[8] - Mass:927367.1499999998 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:171.22, InsertsAfter: 29
 * M[9] - Mass:1024457.95 Overlap:7/7 LogOddsScore:7.539419486497213, SumScore:64.3411337458986, InsertsAfter: 11
 * M[10] - Mass:1080761.3125 Overlap:5/7 LogOddsScore:5.043365737366442, SumScore:38.795, InsertsAfter: 21
 * M[11] - Mass:1167978.384615385 Overlap:4/7 LogOddsScore:6.216823715468156, SumScore:61.882, InsertsAfter: 13
 * M[12] - Mass:1225451.1818181819 Overlap:4/7 LogOddsScore:5.006081289134606, SumScore:43.898, InsertsAfter: 12
 * M[13] - Mass:1280360.833333333 Overlap:3/7 LogOddsScore:2.5473119882356725, SumScore:38.771133745898595, InsertsAfter: 28
 * M[14] - Mass:1345285.0 Overlap:2/5 LogOddsScore:0.7764029907064618, SumScore:21.339, InsertsAfter: 16
 * M[15] - Mass:1413378.8461538462 Overlap:5/5 LogOddsScore:4.520483614402617, SumScore:42.908, InsertsAfter: 24
 * M[16] - Mass:1527662.7500000002 Overlap:4/5 LogOddsScore:4.483199166170781, SumScore:36.575, InsertsAfter: 39
 * M[17] - Mass:1690590.6470588236 Overlap:5/5 LogOddsScore:5.731226040736166, SumScore:44.98, InsertsAfter: 54
 * M[18] - Mass:1915699.5 Overlap:2/5 LogOddsScore:1.9871454170400107, SumScore:19.142, InsertsAfter: 8
 * M[19] - Mass:1933844.2 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:48.502, InsertsAfter: 53
 * M[20] - Mass:2210109.6 Overlap:3/4 LogOddsScore:3.5791024432902576, SumScore:39.538, InsertsAfter: 10
ConsensusPRM: 0 113084 242090 427891 541086 598258 727203 840322 927367 1024457 1080761 1167978 1225451 1280360 1345285 1413378 1527662 1690590 1915699 1933844 2210109 Consensus: 0 113084 242090 427891 541086 598258 727203 840322 927367 1024457 1080761 1167978 1225451 1280360 1345285 1413378 1527662 1690590 1915699 1933844 2210109
De Novo: IEWIGEISP[200.994][187.927]NY[243.254][276.265], Merged: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISP[143.695]G[187.927]NY[243.254][276.265]
-312075 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286 1182354 1239438 1310475 1397507 1496575 1624669 1737753 1824785 1984869 2112963 2184000 2285047 2342068 2505131 2606178 2753246 2854293 2911314 3074377 3260456 3373540 3502582 3688661 3787729 3915823 4043881 4199982 4297034 4354055 4491113 4548134 4661218 4790260 4976339 5089423 5146444 5275486 5388669 5475612 5572587 5629065 5716282 5773755 5828664 5893589 5961682 6075966 6238894 6464003 6482148 6758413 
30.0 86.0445 139.33349999999996 115.9755 149.86849999999998 155.57800000000003 129.6935 159.12099999999998 172.46799999999996 196.829 177.94 184.4035 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 429.2765 381.65783436474646 392.36513374589856 409.2695668729493 404.70956687294927 401.1700000000001 379.0835 237.58063374589858 187.7185 145.09813374589856 155.66 91.03699999999999 114.31049999999999 41.521133745898595 32.121267491797184 51.871401237695764 33.88740123769577 21.806401237695773 11.328401237695768 42.908 33.238133745898594 44.98 9.13140123769577 45.16513374589859 36.20113374589859 
(RIGHT)Round: 2 for seed: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISP[143.695]G[187.927]NY[243.254][276.265]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:102
 Score: 164.72, AlignedPeaks: 485171 598264 685282 782406 926451 983438 1171424 1285555 1448549 1691637 1967836 
0 203625 220171 239097 299048 304368 309167 311092 323243 327206 339284 349629 350218 354815 355237 356034 365992 367393 368119 385690 386201 440211 457214 479215 485171 495186 497309 553477 570210 572081 598264 608267 614334 616312 685282 703173 722272 743490 760263 777990 778603 779373 782406 839161 839417 885333 885697 907296 926451 948501 965466 983438 999382 1035366 1039318 1058704 1070373 1100467 1103028 1118471 1131522 1171424 1187407 1205374 1222339 1234688 1244437 1285555 1327707 1331645 1384298 1388452 1392850 1427774 1428057 1448549 1485552 1513564 1562555 1572565 1598759 1600630 1616731 1617363 1668550 1673531 1673820 1675654 1685665 1691637 1730629 1758788 1802705 1803447 1820630 1831556 1871792 1950669 1951531 1951954 1967215 1967836 2152830 
15.0 5.069 3.65 4.787 12.287 0.344 0.457 1.148 0.43 4.245 2.637 7.578 16.307 4.221 4.128 8.064 6.909 1.912 14.388 4.147 2.233 1.584 5.18 15.332 25.784 0.544 0.087 0.007 0.824 2.291 20.273 3.713 0.154 1.288 23.948 0.385 8.447 0.091 3.992 0.097 5.615 5.015 8.539 6.087 4.39 4.047 3.33 2.004 16.455 0.875 0.254 15.254 7.262 2.643 1.188 2.341 1.275 0.546 10.731 1.0 0.856 11.285 7.18 0.966 0.783 8.14 12.906 7.259 0.4 3.553 4.157 2.393 0.271 1.823 2.676 10.095 4.753 1.084 5.39 7.081 1.101 3.753 4.94 1.031 0.571 1.685 1.635 1.063 19.358 14.35 0.271 1.31 9.884 4.348 17.661 0.902 12.419 6.256 1.083 1.96 2.006 11.478 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1050_0.prm:16
 Score: 160.94500000000002, AlignedPeaks: 485106 598122 685184 782276 926309 1171432 1285398 1448458 1691619 1967739 
0 144132 185507 293065 297212 298941 299632 309065 310986 315895 316668 323180 327855 341339 351201 356078 368108 422144 425367 439152 440148 445199 454267 457094 485106 551310 570184 572187 596063 598122 598685 616170 665298 683143 685184 701060 703280 705560 721269 782276 813181 814258 827465 828365 839317 907031 926309 942318 960180 960871 964489 978375 983281 1030406 1033180 1040690 1043357 1047961 1065757 1070361 1074144 1074807 1130486 1152848 1171432 1187441 1206186 1215129 1274406 1285398 1286254 1299460 1300537 1331458 1355165 1355909 1399167 1428532 1448458 1456457 1515625 1541531 1543534 1559548 1560467 1562479 1610694 1628639 1630860 1656619 1673616 1674567 1691619 1701571 1745610 1790538 1802783 1814086 1814793 1820656 1939383 1951894 1967739 2095708 
15.0 0.888 2.998 10.849 3.827 16.901 9.751 3.195 10.204 4.219 5.045 1.891 3.613 5.196 0.954 5.173 1.752 16.383 0.649 4.774 8.589 2.049 0.979 13.92 20.654 3.852 0.934 1.965 1.465 18.081 7.289 2.086 4.972 0.409 24.346 1.366 4.235 0.208 0.884 13.269 2.18 0.836 0.218 8.415 10.472 1.712 16.222 9.608 1.157 0.244 0.557 1.171 9.737 0.715 0.917 0.294 0.513 1.345 0.364 3.159 11.368 6.977 2.923 0.648 10.408 9.041 11.55 2.292 6.441 12.864 0.747 2.57 1.342 3.229 2.111 2.997 6.205 2.603 12.031 2.792 6.732 1.895 4.418 4.807 2.717 6.569 0.738 13.826 0.49 5.508 17.457 1.139 14.005 0.15 0.397 1.959 10.872 2.154 22.102 10.405 2.935 3.376 19.065 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1050_0.prm:62
 Score: 158.244, AlignedPeaks: 485171 598255 685271 782326 926389 983417 1171490 1285531 1448577 1691643 1967681 
0 144093 163347 293006 293577 297137 299006 309292 310025 311292 315972 316997 323324 328074 351095 356166 368215 422257 439144 439950 445145 457085 466973 483052 485171 502835 551344 570167 572187 596153 598255 598924 616326 665233 683216 685271 701212 703173 715374 780317 782326 813387 814286 828348 839361 889419 924980 925731 926389 929670 942328 943060 943417 983417 1015761 1024903 1042233 1043423 1070397 1073812 1074611 1083090 1130404 1170403 1170760 1171490 1187421 1206053 1206420 1215276 1274469 1285531 1291121 1299279 1299534 1300433 1331494 1333503 1355819 1399359 1408362 1428541 1448577 1456551 1515550 1541633 1543653 1546785 1559688 1560002 1560504 1562498 1610985 1628658 1630768 1656681 1673870 1691643 1709690 1745605 1757690 1762725 1790496 1802528 1803795 1804528 1814828 1820809 1822694 1949179 1951778 1967681 2095810 
15.0 0.7 1.018 10.34 3.921 2.863 19.245 4.88 5.108 3.988 6.012 6.021 1.507 2.807 0.42 7.088 0.75 16.364 2.574 6.521 2.448 16.464 2.05 2.458 19.785 1.6 4.487 0.151 1.334 2.416 19.955 2.051 0.652 3.222 6.263 24.079 1.146 2.404 0.13 1.518 6.45 0.96 0.394 6.234 13.335 0.062 2.835 1.226 15.912 1.141 7.84 1.747 0.065 9.433 1.472 0.667 2.126 0.621 2.883 4.709 9.118 0.922 5.349 1.81 2.703 9.861 8.956 7.797 8.621 3.619 4.204 10.852 3.101 0.608 0.852 1.252 0.102 0.363 4.699 6.427 2.071 3.266 12.364 2.31 5.199 2.545 2.79 1.049 3.348 4.696 2.702 5.202 1.913 12.308 0.208 8.737 2.326 12.307 0.021 1.174 2.474 1.616 0.591 0.724 0.425 1.955 21.623 11.45 0.323 3.15 2.139 17.246 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_950_0.prm:64
 Score: 146.174, AlignedPeaks: 299133 412052 499208 596272 740352 797408 985232 1099524 1262388 1505627 
0 127612 129213 143925 162906 275754 277344 282217 292173 293220 299133 308855 310023 310729 316296 323007 325871 328432 329058 367953 386338 412052 412668 422196 430046 453164 499208 515312 517205 535038 539978 551314 592048 596272 627262 628185 653238 665355 683172 722258 740352 779322 791357 793009 797408 828200 853991 884277 898355 907210 910036 932911 937286 941775 955132 980698 981681 985232 985967 987244 990456 994831 1017706 1020532 1029387 1043455 1066872 1073751 1099524 1113421 1130333 1148420 1164265 1169847 1178959 1187329 1213315 1218229 1222474 1229857 1249347 1262388 1274503 1291424 1299557 1300480 1331460 1335694 1376399 1392704 1405895 1412430 1428526 1446794 1456580 1473502 1474578 1491764 1505627 1515074 1515681 1543592 1559789 1604735 1628657 1634574 1635569 1645525 1651988 1746812 1781454 1909731 
15.0 0.31 3.725 0.819 6.41 5.162 4.772 1.114 3.865 10.793 13.974 4.026 4.071 2.434 0.815 0.568 0.544 0.872 2.431 0.531 2.063 22.943 17.08 11.129 8.219 0.069 26.183 2.168 11.215 0.76 2.328 9.045 0.479 14.604 4.044 0.817 7.442 9.777 0.969 0.315 15.731 2.659 1.182 1.439 14.462 3.532 1.79 9.802 0.083 0.548 0.447 0.199 0.32 0.683 0.834 2.703 8.632 4.883 1.443 0.325 2.569 1.312 0.77 1.77 0.429 1.985 3.534 1.293 7.184 4.355 3.762 0.352 2.707 12.59 2.878 8.439 8.189 1.02 3.629 0.353 1.149 14.686 4.044 0.321 1.237 0.79 2.294 0.843 8.798 1.099 0.829 0.575 4.88 0.094 1.543 1.653 0.476 1.297 11.524 0.723 16.382 4.445 6.663 1.818 13.916 14.286 3.692 1.189 3.713 2.67 15.789 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1150_0.prm:2
 Score: 145.90699999999998, AlignedPeaks: 485154 598179 685170 782282 926291 983367 1171558 1285382 1448492 1691567 1967654 
0 315648 317072 323042 329957 330746 331183 331925 333968 334939 339238 341134 346949 348827 351211 355882 365011 366963 367763 386406 394320 412305 424980 440329 457308 461515 476045 478241 483093 485154 495171 496977 502961 570274 571629 572263 589391 595941 598179 607286 614134 616234 683217 685170 701180 703195 725917 736357 782282 798258 798878 801367 813384 830762 839120 850393 888370 926291 944132 953633 971745 982375 983367 1013453 1015356 1018367 1035276 1054307 1056768 1070308 1085446 1128697 1131175 1140301 1140940 1158536 1166957 1167662 1170140 1171558 1176066 1213391 1242069 1263561 1285382 1298293 1298991 1307310 1307984 1327092 1391671 1400864 1448492 1456649 1457453 1466052 1485453 1491814 1494975 1499959 1500579 1562461 1572920 1597665 1613670 1684703 1691567 1700667 1709446 1726574 1727208 1728563 1744742 1745531 1813674 1820641 1841529 1858508 1873857 1912431 1950010 1951888 1957703 1959599 1966912 1967654 1968091 1968880 1975795 1981765 1983189 2280826 
15.0 6.054 4.896 1.064 7.083 15.671 15.727 7.765 4.38 3.572 3.064 3.393 5.337 14.003 3.128 9.681 4.624 4.915 3.484 1.832 0.041 1.577 0.65 2.111 3.378 4.193 4.587 13.658 4.2 21.662 4.674 3.148 8.368 1.271 2.798 3.056 1.441 2.18 19.418 9.329 2.478 5.965 3.766 25.442 5.003 8.075 1.171 3.997 7.212 0.244 0.531 1.585 2.923 0.378 4.623 7.81 3.566 9.232 0.467 0.633 0.517 1.015 5.961 7.939 1.881 0.422 0.673 2.979 0.812 4.324 0.441 0.725 0.532 0.779 0.366 0.572 10.497 0.401 1.097 2.872 1.292 1.73 1.146 0.379 11.71 10.794 8.368 2.913 1.906 1.95 3.454 1.369 14.172 1.525 1.009 0.405 1.261 6.077 1.52 0.031 4.061 7.968 0.763 2.357 3.072 0.698 9.866 7.371 1.48 1.412 0.905 3.67 5.398 2.472 20.954 14.445 0.37 2.055 1.886 0.955 6.381 0.39 0.948 5.052 1.973 18.36 18.05 7.796 0.936 5.939 2.017 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:257.51899999999995, InsertsAfter: 32
 * M[1] - Mass:113048.93333333333 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:191.70700000000002, InsertsAfter: 19
 * M[2] - Mass:200089.86666666667 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:238.3085, InsertsAfter: 25
 * M[3] - Mass:297172.8 Overlap:7/7 LogOddsScore:11.17164676549786, SumScore:91.5951337458986, InsertsAfter: 14
 * M[4] - Mass:354110.7142857143 Overlap:5/7 LogOddsScore:5.043365737366442, SumScore:41.958999999999996, InsertsAfter: 13
 * M[5] - Mass:441197.13333333324 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:125.42340123769577, InsertsAfter: 18
 * M[6] - Mass:498235.8666666667 Overlap:7/7 LogOddsScore:11.17164676549786, SumScore:88.73440123769578, InsertsAfter: 22
 * M[7] - Mass:585200.8888888889 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:21.442999999999998, InsertsAfter: 1
 * M[8] - Mass:589349.5 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:20.486, InsertsAfter: 29
 * M[9] - Mass:686271.4 Overlap:7/7 LogOddsScore:8.750161912830762, SumScore:82.217, InsertsAfter: 28
 * M[10] - Mass:800351.6 Overlap:7/7 LogOddsScore:9.96090433916431, SumScore:83.10713374589861, InsertsAfter: 44
 * M[11] - Mass:963359.5999999996 Overlap:7/7 LogOddsScore:11.17164676549786, SumScore:108.328, InsertsAfter: 30
 * M[12] - Mass:1077334.1111111112 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:33.92700000000001, InsertsAfter: 14
 * M[13] - Mass:1143510.0 Overlap:2/7 LogOddsScore:1.2992851136702874, SumScore:26.134, InsertsAfter: 10
 * M[14] - Mass:1188533.2727272727 Overlap:3/7 LogOddsScore:2.5473119882356725, SumScore:21.418000000000003, InsertsAfter: 5
 * M[15] - Mass:1206493.0 Overlap:7/7 LogOddsScore:11.17164676549786, SumScore:107.2171337458986, InsertsAfter: 22
 * M[16] - Mass:1317522.6666666665 Overlap:3/7 LogOddsScore:1.3365695619021236, SumScore:21.48, InsertsAfter: 4
 * M[17] - Mass:1329511.111111111 Overlap:4/7 LogOddsScore:7.427566141801704, SumScore:78.595, InsertsAfter: 0
 * M[18] - Mass:1335522.7857142857 Overlap:5/7 LogOddsScore:7.4648505900335405, SumScore:68.24700000000001, InsertsAfter: 24
 * M[19] - Mass:1482586.0666666667 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:118.13913374589859, InsertsAfter: 5
 * M[20] - Mass:1610614.875 Overlap:3/5 LogOddsScore:5.6566571442724936, SumScore:45.0, InsertsAfter: 2
ConsensusPRM: 0 113048 200089 297172 354110 441197 498235 585200 589349 686271 800351 963359 1077334 1143510 1188533 1206493 1317522 1329511 1335522 1482586 1610614 Consensus: 0 113048 200089 297172 354110 441197 498235 585200 589349 686271 800351 963359 1077334 1143510 1188533 1206493 1317522 1329511 1335522 1482586 1610614
De Novo: ISPGSGSTNYNEEFQ, Merged: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISPGSGSTNYNEEFQ
-312075 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286 1182354 1239438 1310475 1397507 1496575 1624669 1737753 1824785 1984869 2112963 2184000 2285047 2342068 2505131 2606178 2753246 2854293 2911314 3074377 3260456 3373540 3502582 3688661 3787729 3915823 4043881 4199982 4297034 4354055 4491113 4548134 4661218 4790260 4976339 5089423 5146444 5275486 5388669 5475612 5572587 5629937 5716282 5717024 5773755 5861027 5865176 5961682 6075966 6238894 6353161 6419337 6464360 6482148 6593349 6605338 6611349 6758413 6886441 
30.0 86.0445 139.33349999999996 115.9755 149.86849999999998 155.57800000000003 129.6935 159.12099999999998 172.46799999999996 196.829 177.94 184.4035 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 429.2765 381.65783436474646 392.36513374589856 409.2695668729493 404.70956687294927 401.1700000000001 379.0835 237.58063374589858 187.7185 145.09813374589856 206.5895 141.372 176.3095 66.5581337458986 35.28526749179718 51.871401237695764 125.42340123769577 61.310901237695774 14.769267491797178 3.8016687294929525 62.5625 58.1726337458986 76.654 27.25326749179719 9.449668729492952 8.070534983594364 76.1911337458986 8.132534983594361 68.58440123769577 61.573267491797196 77.1701337458986 38.32626749179718 
(RIGHT)Round: 3 for seed: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISPGSGSTNYNEEFQ
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_950_0.prm:64
 Score: 147.14499999999998, AlignedPeaks: 740352 797408 884277 985232 1099524 1262388 1376399 1505627 1634574 1781454 1909731 
0 127612 129213 143925 162906 275754 277344 282217 292173 293220 299133 308855 310023 310729 316296 323007 325871 328432 329058 367953 386338 412052 412668 422196 430046 453164 499208 515312 517205 535038 539978 551314 592048 596272 627262 628185 653238 665355 683172 722258 740352 779322 791357 793009 797408 828200 853991 884277 898355 907210 910036 932911 937286 941775 955132 980698 981681 985232 985967 987244 990456 994831 1017706 1020532 1029387 1043455 1066872 1073751 1099524 1113421 1130333 1148420 1164265 1169847 1178959 1187329 1213315 1218229 1222474 1229857 1249347 1262388 1274503 1291424 1299557 1300480 1331460 1335694 1376399 1392704 1405895 1412430 1428526 1446794 1456580 1473502 1474578 1491764 1505627 1515074 1515681 1543592 1559789 1604735 1628657 1634574 1635569 1645525 1651988 1746812 1781454 1909731 
15.0 0.31 3.725 0.819 6.41 5.162 4.772 1.114 3.865 10.793 13.974 4.026 4.071 2.434 0.815 0.568 0.544 0.872 2.431 0.531 2.063 22.943 17.08 11.129 8.219 0.069 26.183 2.168 11.215 0.76 2.328 9.045 0.479 14.604 4.044 0.817 7.442 9.777 0.969 0.315 15.731 2.659 1.182 1.439 14.462 3.532 1.79 9.802 0.083 0.548 0.447 0.199 0.32 0.683 0.834 2.703 8.632 4.883 1.443 0.325 2.569 1.312 0.77 1.77 0.429 1.985 3.534 1.293 7.184 4.355 3.762 0.352 2.707 12.59 2.878 8.439 8.189 1.02 3.629 0.353 1.149 14.686 4.044 0.321 1.237 0.79 2.294 0.843 8.798 1.099 0.829 0.575 4.88 0.094 1.543 1.653 0.476 1.297 11.524 0.723 16.382 4.445 6.663 1.818 13.916 14.286 3.692 1.189 3.713 2.67 15.789 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1050_0.prm:16
 Score: 144.465, AlignedPeaks: 926309 983281 1070361 1171432 1285398 1448458 1562479 1691619 1820656 1967739 2095708 
0 144132 185507 293065 297212 298941 299632 309065 310986 315895 316668 323180 327855 341339 351201 356078 368108 422144 425367 439152 440148 445199 454267 457094 485106 551310 570184 572187 596063 598122 598685 616170 665298 683143 685184 701060 703280 705560 721269 782276 813181 814258 827465 828365 839317 907031 926309 942318 960180 960871 964489 978375 983281 1030406 1033180 1040690 1043357 1047961 1065757 1070361 1074144 1074807 1130486 1152848 1171432 1187441 1206186 1215129 1274406 1285398 1286254 1299460 1300537 1331458 1355165 1355909 1399167 1428532 1448458 1456457 1515625 1541531 1543534 1559548 1560467 1562479 1610694 1628639 1630860 1656619 1673616 1674567 1691619 1701571 1745610 1790538 1802783 1814086 1814793 1820656 1939383 1951894 1967739 2095708 
15.0 0.888 2.998 10.849 3.827 16.901 9.751 3.195 10.204 4.219 5.045 1.891 3.613 5.196 0.954 5.173 1.752 16.383 0.649 4.774 8.589 2.049 0.979 13.92 20.654 3.852 0.934 1.965 1.465 18.081 7.289 2.086 4.972 0.409 24.346 1.366 4.235 0.208 0.884 13.269 2.18 0.836 0.218 8.415 10.472 1.712 16.222 9.608 1.157 0.244 0.557 1.171 9.737 0.715 0.917 0.294 0.513 1.345 0.364 3.159 11.368 6.977 2.923 0.648 10.408 9.041 11.55 2.292 6.441 12.864 0.747 2.57 1.342 3.229 2.111 2.997 6.205 2.603 12.031 2.792 6.732 1.895 4.418 4.807 2.717 6.569 0.738 13.826 0.49 5.508 17.457 1.139 14.005 0.15 0.397 1.959 10.872 2.154 22.102 10.405 2.935 3.376 19.065 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1050_0.prm:62
 Score: 137.51, AlignedPeaks: 926389 983417 1070397 1171490 1285531 1448577 1562498 1691643 1820809 1967681 2095810 
0 144093 163347 293006 293577 297137 299006 309292 310025 311292 315972 316997 323324 328074 351095 356166 368215 422257 439144 439950 445145 457085 466973 483052 485171 502835 551344 570167 572187 596153 598255 598924 616326 665233 683216 685271 701212 703173 715374 780317 782326 813387 814286 828348 839361 889419 924980 925731 926389 929670 942328 943060 943417 983417 1015761 1024903 1042233 1043423 1070397 1073812 1074611 1083090 1130404 1170403 1170760 1171490 1187421 1206053 1206420 1215276 1274469 1285531 1291121 1299279 1299534 1300433 1331494 1333503 1355819 1399359 1408362 1428541 1448577 1456551 1515550 1541633 1543653 1546785 1559688 1560002 1560504 1562498 1610985 1628658 1630768 1656681 1673870 1691643 1709690 1745605 1757690 1762725 1790496 1802528 1803795 1804528 1814828 1820809 1822694 1949179 1951778 1967681 2095810 
15.0 0.7 1.018 10.34 3.921 2.863 19.245 4.88 5.108 3.988 6.012 6.021 1.507 2.807 0.42 7.088 0.75 16.364 2.574 6.521 2.448 16.464 2.05 2.458 19.785 1.6 4.487 0.151 1.334 2.416 19.955 2.051 0.652 3.222 6.263 24.079 1.146 2.404 0.13 1.518 6.45 0.96 0.394 6.234 13.335 0.062 2.835 1.226 15.912 1.141 7.84 1.747 0.065 9.433 1.472 0.667 2.126 0.621 2.883 4.709 9.118 0.922 5.349 1.81 2.703 9.861 8.956 7.797 8.621 3.619 4.204 10.852 3.101 0.608 0.852 1.252 0.102 0.363 4.699 6.427 2.071 3.266 12.364 2.31 5.199 2.545 2.79 1.049 3.348 4.696 2.702 5.202 1.913 12.308 0.208 8.737 2.326 12.307 0.021 1.174 2.474 1.616 0.591 0.724 0.425 1.955 21.623 11.45 0.323 3.15 2.139 17.246 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_700_0.prm:236
 Score: 127.44299999999998, AlignedPeaks: 926537 983681 1070458 1171606 1285671 1448708 1562726 1691983 1820700 2095965 
0 146597 211295 225836 229401 293303 298125 299212 316829 339208 356147 412269 422060 457517 471196 485154 501408 519650 524244 532190 550356 555131 576971 580074 598181 616496 633970 649291 665269 669433 685321 692837 702391 703638 721581 724463 740090 743711 744490 758005 782337 805306 814530 818451 828253 831493 846027 891558 898573 907300 909073 925889 926537 942312 944397 978541 983681 984364 1019497 1043452 1053436 1070458 1094479 1129611 1130362 1135435 1169579 1171606 1187439 1188087 1204903 1206051 1206676 1215402 1222418 1224326 1267960 1285671 1299445 1308670 1355971 1373885 1389513 1392395 1410338 1421139 1428655 1429322 1448708 1480005 1497480 1515795 1533901 1537005 1562726 1563620 1566587 1581786 1589732 1594326 1612568 1628822 1642780 1659734 1691983 1699786 1701707 1709698 1728773 1757828 1774767 1798024 1814666 1820700 1842734 1859865 1884574 1888140 1967378 2095965 
15.0 5.17 0.602 3.172 2.946 7.962 0.604 24.407 9.855 1.835 0.038 1.501 11.395 1.025 0.567 8.446 1.17 1.284 0.902 0.467 2.723 0.285 0.384 3.368 19.409 7.703 6.413 1.707 8.998 0.258 1.387 1.548 1.696 5.004 2.185 4.335 3.893 3.738 4.132 3.061 0.106 0.46 0.174 1.305 11.816 0.959 14.7 3.413 0.374 2.182 4.771 12.014 4.167 10.435 4.674 2.693 9.893 5.452 3.927 11.546 1.561 13.924 0.951 4.887 9.055 1.269 4.501 16.975 2.303 11.748 8.694 5.512 2.185 1.82 3.664 0.253 11.342 19.391 2.062 1.145 5.467 3.895 8.078 3.848 6.239 2.198 5.314 8.613 9.753 6.821 7.959 27.679 8.254 1.664 2.32 2.418 1.15 2.953 0.481 1.424 2.677 9.15 0.369 1.002 11.336 1.187 0.75 1.152 0.662 0.226 0.943 3.284 16.34 9.684 5.308 1.835 0.063 1.012 5.727 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:193
 Score: 121.89699999999999, AlignedPeaks: 1542720 1599601 1686747 1787780 1901840 2064792 2178670 2307715 2436794 2712057 
0 163011 289522 292677 293273 299298 301333 317066 374336 385202 386099 404172 422332 457763 469095 486369 488448 527249 536710 549885 550912 551397 598211 616356 641767 650964 665275 705514 714330 714938 757762 758419 762611 771516 800038 802310 814519 828227 843451 884964 892336 894096 898325 915388 931700 942289 950997 964170 972289 1032586 1043319 1054570 1057102 1075635 1077532 1089335 1090091 1097135 1100309 1101409 1101885 1119167 1130481 1135375 1153850 1154606 1187333 1212379 1214412 1218695 1230546 1232534 1251063 1273715 1274369 1283528 1299451 1301555 1317522 1319510 1331563 1398504 1410557 1412545 1428526 1430616 1446539 1455865 1456352 1479004 1497533 1511372 1515601 1517688 1542720 1575461 1576217 1599601 1610900 1628182 1628658 1639976 1640732 1652535 1654432 1672965 1675497 1686747 1697481 1757742 1765897 1779070 1787780 1798367 1814677 1831742 1835971 1837731 1845103 1886616 1901840 1915548 1927757 1930029 1958551 1967456 1971648 1972305 1981097 2015129 2015737 2024553 2033044 2064792 2079103 2088300 2113711 2122688 2131856 2136505 2178670 2179155 2193357 2202818 2241619 2243698 2272304 2307715 2325895 2328252 2328894 2343968 2344865 2355731 2413001 2428734 2430769 2436794 2440545 2458789 2548738 2584390 2712057 
15.0 1.769 3.849 2.419 9.356 3.932 4.795 1.965 2.977 0.7 1.259 3.453 8.819 3.853 2.217 2.33 3.726 3.285 2.958 0.538 1.272 1.469 1.427 8.471 2.516 0.457 9.31 2.559 1.998 3.278 1.028 2.147 3.175 2.559 2.477 7.747 2.73 7.22 4.937 3.247 3.351 3.36 11.336 13.127 2.717 10.241 0.938 1.844 7.177 4.061 6.826 1.47 2.897 1.827 1.622 1.831 2.34 0.864 3.291 7.547 12.373 3.665 9.315 2.72 1.447 1.228 11.311 1.932 18.805 1.859 0.926 13.512 1.505 5.577 6.591 7.02 4.78 27.134 1.242 10.423 1.977 2.338 4.311 2.541 26.602 5.975 13.59 7.992 4.357 0.665 9.273 2.728 22.377 1.734 16.094 0.804 0.032 10.266 0.661 17.567 19.149 1.963 1.402 0.279 1.678 3.525 1.03 6.635 4.424 10.982 1.178 0.525 12.671 2.029 23.394 14.179 2.11 3.473 2.681 5.387 10.343 3.104 8.433 3.13 4.851 3.3 3.684 3.947 4.738 4.098 7.507 3.428 1.211 9.854 4.555 3.36 6.443 5.0 1.385 1.662 7.967 7.964 2.14 0.762 1.246 2.468 2.662 7.964 1.742 0.711 1.234 1.39 0.537 1.584 1.077 0.073 0.691 10.103 1.605 0.578 1.886 6.777 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:193.54940123769578, InsertsAfter: 17
 * M[1] - Mass:56968.666666666664 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:115.10190123769577, InsertsAfter: 25
 * M[2] - Mass:143989.33333333337 Overlap:7/7 LogOddsScore:7.539419486497213, SumScore:51.17226749179718, InsertsAfter: 28
 * M[3] - Mass:244981.83333333334 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:117.3605, InsertsAfter: 35
 * M[4] - Mass:359099.8333333333 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:118.80663374589862, InsertsAfter: 52
 * M[5] - Mass:522081.0 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:135.342, InsertsAfter: 31
 * M[6] - Mass:636100.3333333333 Overlap:7/7 LogOddsScore:8.750161912830762, SumScore:58.10926749179719, InsertsAfter: 35
 * M[7] - Mass:765234.0 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:133.3271337458986, InsertsAfter: 38
 * M[8] - Mass:894258.5 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:117.5012674917972, InsertsAfter: 16
 * M[9] - Mass:1041287.3333333333 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:141.77413374589858, InsertsAfter: 0
 * M[10] - Mass:1169396.8333333335 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:113.32626749179718, InsertsAfter: 0
ConsensusPRM: 0 56968 143989 244981 359099 522081 636100 765234 894258 1041287 1169396 Consensus: 0 56968 143989 244981 359099 522081 636100 765234 894258 1041287 1169396
De Novo: GSTNYNEEFK, Merged: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISPGSGSTNYNEEFQ
-312075 0 112978 240984 369061 456095 513066 584070 713123 826229 957156 1085286 1182354 1239438 1310475 1397507 1496575 1624669 1737753 1824785 1984869 2112963 2184000 2285047 2342068 2505131 2606178 2753246 2854293 2911314 3074377 3260456 3373540 3502582 3688661 3787729 3915823 4043881 4199982 4297034 4354055 4491113 4548134 4661218 4790260 4976339 5089423 5146444 5275486 5388669 5475612 5572587 5629937 5717024 5773755 5861027 5961682 6075966 6238894 6353161 6482148 6611349 6758413 6886441 
30.0 86.0445 139.33349999999996 115.9755 149.86849999999998 155.57800000000003 129.6935 159.12099999999998 172.46799999999996 196.829 177.94 184.4035 116.6755 120.0 120.0 150.0 150.0 105.0 60.0 60.0 45.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 30.0 60.0 210.0 300.0 300.0 390.0 435.0 435.0 450.0 390.0 429.2765 381.65783436474646 392.36513374589856 409.2695668729493 404.70956687294927 401.1700000000001 379.0835 237.58063374589858 187.7185 145.09813374589856 206.5895 141.372 176.3095 66.5581337458986 35.28526749179718 159.48640123769576 88.20640123769577 32.970767491797176 89.9615 88.48963374589862 105.998 42.681267491797186 104.7591337458986 89.5372674917972 109.47213374589859 75.82626749179718 

(LEFT)Round: 0 for seed: NEKFKGKATFTADWSSN
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:387
 Score: 95.649, AlignedPeaks: 1204378 1318416 1447461 1575566 
0 103009 189972 199993 259615 261089 278047 279150 300644 301139 389198 401262 402102 407123 419042 423128 459144 485286 516116 517245 518236 536166 594255 630213 632256 648181 650190 666118 668212 717287 762258 774277 779273 795232 797284 815256 832201 861248 878243 935549 935986 936298 944557 944860 975371 991593 993365 1000667 1018352 1027071 1057339 1068721 1119353 1122267 1155405 1204378 1206429 1221320 1242366 1300455 1318416 1319376 1320504 1336379 1351335 1356389 1377479 1429498 1434519 1447461 1535483 1553399 1557471 1558575 1575566 1577006 1646650 1690477 1818611 
15.0 0.235 1.155 6.782 8.236 18.227 16.401 2.323 4.779 8.346 19.814 4.661 15.004 12.116 0.139 0.243 10.777 0.005 2.948 7.711 18.035 1.522 0.139 15.259 15.261 0.938 4.641 0.849 2.026 10.084 0.448 3.564 11.15 0.795 3.484 3.477 2.368 15.231 2.393 5.239 3.346 2.869 3.262 3.262 0.951 2.771 0.088 0.765 3.13 2.569 23.768 2.097 5.11 1.521 1.533 20.093 6.937 0.139 0.677 1.854 21.712 8.171 1.04 3.326 1.436 0.387 2.544 0.635 0.252 25.266 1.67 0.524 2.138 3.95 28.578 12.222 1.997 8.721 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:204
 Score: 88.805, AlignedPeaks: 1176488 1290626 1419789 1547789 1694761 
0 174027 207981 214268 242128 245355 257209 298667 300287 304374 316140 400208 409286 411297 413231 430180 446325 483412 522140 530675 543386 550454 559570 560375 561236 577348 588441 600920 620901 663296 671644 672471 680415 681910 690355 706627 708145 730442 765068 773969 802750 817468 818346 836616 846025 847464 860777 877370 895212 904079 947491 990469 1007537 1015082 1023680 1032059 1061553 1101491 1116749 1118544 1119532 1121397 1136655 1176488 1206087 1230544 1241810 1247675 1277079 1290626 1334067 1342934 1360768 1377369 1390682 1395535 1398664 1399403 1419789 1420678 1435396 1464177 1503430 1528153 1530001 1531519 1536764 1547789 1557731 1565675 1566502 1574850 1614191 1632000 1637226 1649705 1674529 1676910 1677771 1678575 1687692 1690607 1694761 1707471 1716006 1742885 1756786 1808053 1824915 1826849 1828860 1837263 1837938 1922080 1928773 1933772 1937859 1938823 1939479 1942864 1955046 1980936 1992712 2023878 2030164 2064118 2220135 
15.0 6.36 0.568 0.808 1.036 8.489 3.703 0.668 1.995 1.391 13.387 2.761 0.643 1.277 1.194 12.364 0.669 1.44 0.859 5.06 14.139 1.418 11.331 14.418 9.19 0.897 2.162 5.538 0.033 1.926 0.611 2.589 0.347 0.042 10.483 7.13 8.072 0.399 1.028 0.715 2.759 5.204 21.276 0.991 1.371 2.267 6.485 17.743 6.481 0.557 13.075 13.385 2.648 0.938 1.364 2.647 14.272 6.002 4.816 24.535 21.312 2.079 8.683 11.574 3.977 2.759 0.243 20.493 0.658 11.629 2.711 9.75 15.343 12.933 2.725 1.144 5.9 2.75 25.764 2.535 4.039 1.617 2.287 2.265 2.825 5.26 1.066 18.104 0.791 7.192 1.527 2.131 1.201 0.05 7.726 2.186 3.132 6.404 13.718 15.621 1.482 0.967 21.734 3.112 1.711 1.422 1.664 17.755 0.412 0.73 1.401 0.775 1.484 15.814 0.362 0.834 5.294 0.748 0.432 0.417 0.456 0.652 9.457 0.554 1.814 7.006 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:34
 Score: 87.25, AlignedPeaks: 1379591 1508613 1784082 1911716 
0 146798 211996 216107 226123 256214 257194 273724 274212 315257 338771 384007 389083 401848 458889 467806 494628 500431 501136 503166 503817 515946 517215 525403 597056 603981 607461 616498 625229 625833 645668 675482 677311 695698 774220 804345 806293 823200 823887 824330 833608 834615 842684 883585 898471 903506 935398 953306 971736 1004445 1006351 1019565 1050505 1067374 1068141 1117787 1135423 1161311 1165653 1179449 1181483 1209367 1229826 1232580 1250436 1282422 1287457 1293887 1302343 1343244 1351313 1352320 1361598 1362041 1379591 1381583 1396705 1407925 1431045 1431687 1468855 1490230 1491610 1508613 1510446 1521342 1529169 1534701 1540260 1560095 1560699 1569430 1578467 1588872 1596065 1604794 1660525 1668713 1669982 1682111 1682762 1684792 1685497 1691300 1718122 1727039 1782821 1784082 1791589 1796906 1801921 1828852 1847157 1911716 1912204 1928734 1929713 1947614 1959805 1969826 1973932 2023730 2039130 2167917 
15.0 3.276 1.381 12.833 2.572 0.058 1.249 13.075 15.775 2.609 2.016 1.39 12.185 18.941 0.173 0.573 2.418 8.959 7.366 2.763 1.414 4.75 7.515 0.974 0.522 0.098 8.621 1.451 1.752 0.765 0.447 2.968 14.564 0.361 0.936 4.341 19.938 1.528 3.446 3.776 1.929 2.979 0.831 4.43 0.078 2.352 16.612 16.337 2.914 1.614 18.552 2.441 14.158 0.824 2.432 1.027 13.382 2.107 3.562 18.28 2.64 0.108 0.232 17.335 21.962 0.384 0.82 2.964 5.148 2.431 5.252 1.427 7.222 3.686 26.985 6.992 6.256 6.963 0.44 0.744 1.712 0.101 0.367 21.94 0.84 0.391 0.883 1.029 0.267 1.827 1.71 3.268 8.181 1.102 4.936 0.009 0.94 8.751 7.085 0.669 1.721 7.59 7.933 1.27 1.617 1.461 3.849 9.796 1.149 12.628 5.192 0.456 0.28 13.529 12.295 3.976 0.372 0.027 0.688 7.85 0.315 1.854 4.669 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_750_0.prm:22
 Score: 83.875, AlignedPeaks: 1230585 1344579 1473707 1601671 1748676 1877120 
0 173700 216859 239315 242241 257220 259957 281229 282078 288128 299113 300273 385168 386299 395526 401302 402242 402916 403562 413012 416055 419996 465328 514096 515354 516582 522212 538450 551611 572605 578179 586071 586918 615243 661206 662356 672142 693451 703334 708044 727959 742785 777891 788401 790301 791545 800222 806446 807516 808560 865723 874559 877214 901287 913295 919429 920622 930557 931365 936384 936996 954334 972291 988023 1033386 1043404 1044415 1045165 1050232 1050953 1061610 1077399 1090422 1091190 1119374 1144656 1172840 1173587 1190576 1205298 1213798 1218865 1219550 1220626 1230585 1276007 1327034 1332661 1333473 1342013 1343408 1344579 1350735 1362743 1386861 1389471 1398307 1456514 1457584 1462960 1463808 1472485 1473707 1475629 1486139 1520465 1521245 1591890 1601671 1602824 1620688 1648787 1677112 1677959 1685851 1691425 1712419 1725580 1741817 1747448 1748676 1749934 1765055 1786226 1798702 1847975 1851018 1855498 1860468 1861788 1862728 1868504 1877120 1877731 1878862 1883640 1963757 1964917 1975997 1982801 2004073 2006810 2021789 2047188 2090330 2101906 2117464 2246020 
15.0 2.259 7.764 0.265 1.501 0.404 4.028 0.013 0.029 17.526 1.908 3.297 0.576 0.702 0.839 4.276 15.526 3.813 13.693 2.059 0.948 5.131 2.979 7.586 7.619 4.574 1.26 0.343 1.052 1.801 1.583 1.205 1.161 2.571 4.237 10.901 4.468 0.695 0.943 1.702 0.476 0.348 8.654 2.515 16.571 7.416 1.549 3.721 8.143 3.613 1.764 0.648 5.364 2.346 1.771 14.574 4.844 7.301 10.631 0.627 2.898 2.198 0.34 1.189 11.14 2.166 10.605 1.244 2.633 2.576 2.684 2.896 13.491 12.26 6.64 5.739 6.345 16.358 5.038 0.923 2.224 2.242 15.394 3.949 11.741 0.743 1.85 16.662 12.321 3.341 6.003 19.197 2.51 4.319 5.016 0.479 1.225 8.161 4.142 1.386 0.611 10.735 22.454 2.346 4.854 2.913 3.662 6.795 15.015 1.807 2.184 1.708 2.876 1.604 2.453 2.15 2.022 1.014 0.736 4.34 14.376 9.838 0.413 2.699 1.645 2.209 0.797 0.528 8.867 16.996 0.369 0.184 1.092 0.998 0.841 0.382 1.578 3.124 11.912 1.322 2.012 1.101 0.381 8.787 2.51 1.854 5.817 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_575_0.prm:542
 Score: 77.991, AlignedPeaks: 764309 878309 1135545 1410621 
0 146961 147471 211292 236295 257000 272085 275233 343087 371160 373163 382120 408555 430332 432630 434304 452208 463167 498600 532257 550198 568396 578758 610500 627253 629255 630030 633254 645270 646519 650956 707632 720512 746073 746373 755320 763372 764309 782862 789379 803423 808680 825599 877167 877613 878309 886481 887218 930579 939232 955896 956151 975448 981969 983193 1000459 1001460 1009511 1018458 1018758 1019144 1019434 1020025 1057199 1061655 1113672 1118312 1119561 1131577 1134801 1135545 1137578 1153583 1154331 1188904 1196435 1197162 1205667 1211181 1214633 1232574 1233361 1242494 1264669 1266231 1268585 1277014 1301664 1320999 1321593 1330527 1349675 1356276 1382711 1391663 1410621 1421744 1450110 1459099 1472519 1489607 1490794 1492146 1507832 1528536 1535593 1547124 1617360 1617870 1746821 
15.0 2.829 3.599 0.67 3.763 1.917 0.776 15.539 2.225 0.907 0.728 1.451 1.424 0.689 0.008 0.06 1.166 5.994 6.51 5.305 1.056 1.105 0.27 3.867 3.211 23.159 13.091 0.405 0.992 9.937 2.917 2.082 3.745 1.904 2.929 0.845 7.738 26.127 0.564 9.465 0.037 0.55 0.123 1.955 6.951 17.527 14.82 2.501 0.422 0.054 0.325 0.387 7.839 0.517 0.304 25.124 9.538 3.868 11.192 10.159 5.518 5.143 1.597 4.112 3.097 5.186 1.736 0.025 4.003 19.408 33.285 0.371 7.365 10.388 0.566 0.288 1.756 0.273 0.429 4.259 5.24 0.435 0.228 1.103 1.036 1.181 4.94 4.893 1.98 2.175 2.735 1.684 0.391 0.944 6.346 1.052 0.486 7.707 2.154 1.994 16.103 0.932 0.983 4.487 0.666 3.15 3.709 2.028 3.368 15.0 

SpectrumHMM Model: * M[0] - Mass:-991303.5 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:16.04, InsertsAfter: 15
 * M[1] - Mass:-259358.0 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:21.814, InsertsAfter: 138
 * M[2] - Mass:-85816.6 Overlap:3/3 LogOddsScore:3.923032594975119, SumScore:29.129, InsertsAfter: 29
 * M[3] - Mass:0.0 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:61.834, InsertsAfter: 15
 * M[4] - Mass:114030.0 Overlap:5/5 LogOddsScore:10.827333382150883, SumScore:97.894, InsertsAfter: 19
 * M[5] - Mass:243085.44444444447 Overlap:5/5 LogOddsScore:10.57419574607036, SumScore:99.66, InsertsAfter: 26
 * M[6] - Mass:371152.3333333334 Overlap:4/5 LogOddsScore:8.36856408125195, SumScore:73.593, InsertsAfter: 21
 * M[7] - Mass:518337.8333333333 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:54.172, InsertsAfter: 25
 * M[8] - Mass:646318.5 Overlap:4/4 LogOddsScore:7.24861417052274, SumScore:44.620999999999995, InsertsAfter: 17
 * M[9] - Mass:704048.0 Overlap:1/4 LogOddsScore:-0.12769373217406166, SumScore:7.85, InsertsAfter: 8
 * M[10] - Mass:831455.0 Overlap:2/4 LogOddsScore:3.541817995058421, SumScore:30.0, InsertsAfter: 11
 * M[11] - Mass:902399.0 Overlap:3/4 LogOddsScore:6.000587295957355, SumScore:45.0, InsertsAfter: 3
 * M[12] - Mass:1003539.0 Overlap:2/3 LogOddsScore:3.885748146743283, SumScore:30.0, InsertsAfter: 0
 * M[13] - Mass:1150607.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 1
ConsensusPRM: -991303 -259358 -85816 0 114030 243085 371152 518337 646318 704048 831455 902399 1003539 1150607 Consensus: -991303 -259358 -85816 0 114030 243085 371152 518337 646318 704048 831455 902399 1003539 1150607
De Novo: [259.358]NEQFQ[185.137]ATF, Merged: [259.358]NEQFQGKATFTADTSSN
-991303 -259358 -85816 0 114030 243085 371152 518337 646318 703361 704048 831455 902399 1003539 1150607 1251654 1322691 1437717 1538764 1625796 1712828 1826870 
16.04 21.814 29.129 45.917 63.947 64.83 51.7965 42.086 37.3105 30.0 7.85 30.0 37.5 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 

(LEFT)Round: 1 for seed: [259.358]NEQFQGKATFTADTSSN
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:34
 Score: 105.80199999999999, AlignedPeaks: 1006351 1379591 1508613 1784082 1911716 
0 146798 211996 216107 226123 256214 257194 273724 274212 315257 338771 384007 389083 401848 458889 467806 494628 500431 501136 503166 503817 515946 517215 525403 597056 603981 607461 616498 625229 625833 645668 675482 677311 695698 774220 804345 806293 823200 823887 824330 833608 834615 842684 883585 898471 903506 935398 953306 971736 1004445 1006351 1019565 1050505 1067374 1068141 1117787 1135423 1161311 1165653 1179449 1181483 1209367 1229826 1232580 1250436 1282422 1287457 1293887 1302343 1343244 1351313 1352320 1361598 1362041 1379591 1381583 1396705 1407925 1431045 1431687 1468855 1490230 1491610 1508613 1510446 1521342 1529169 1534701 1540260 1560095 1560699 1569430 1578467 1588872 1596065 1604794 1660525 1668713 1669982 1682111 1682762 1684792 1685497 1691300 1718122 1727039 1782821 1784082 1791589 1796906 1801921 1828852 1847157 1911716 1912204 1928734 1929713 1947614 1959805 1969826 1973932 2023730 2039130 2167917 
15.0 3.276 1.381 12.833 2.572 0.058 1.249 13.075 15.775 2.609 2.016 1.39 12.185 18.941 0.173 0.573 2.418 8.959 7.366 2.763 1.414 4.75 7.515 0.974 0.522 0.098 8.621 1.451 1.752 0.765 0.447 2.968 14.564 0.361 0.936 4.341 19.938 1.528 3.446 3.776 1.929 2.979 0.831 4.43 0.078 2.352 16.612 16.337 2.914 1.614 18.552 2.441 14.158 0.824 2.432 1.027 13.382 2.107 3.562 18.28 2.64 0.108 0.232 17.335 21.962 0.384 0.82 2.964 5.148 2.431 5.252 1.427 7.222 3.686 26.985 6.992 6.256 6.963 0.44 0.744 1.712 0.101 0.367 21.94 0.84 0.391 0.883 1.029 0.267 1.827 1.71 3.268 8.181 1.102 4.936 0.009 0.94 8.751 7.085 0.669 1.721 7.59 7.933 1.27 1.617 1.461 3.849 9.796 1.149 12.628 5.192 0.456 0.28 13.529 12.295 3.976 0.372 0.027 0.688 7.85 0.315 1.854 4.669 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:387
 Score: 98.911, AlignedPeaks: 944860 1204378 1318416 1447461 1575566 
0 103009 189972 199993 259615 261089 278047 279150 300644 301139 389198 401262 402102 407123 419042 423128 459144 485286 516116 517245 518236 536166 594255 630213 632256 648181 650190 666118 668212 717287 762258 774277 779273 795232 797284 815256 832201 861248 878243 935549 935986 936298 944557 944860 975371 991593 993365 1000667 1018352 1027071 1057339 1068721 1119353 1122267 1155405 1204378 1206429 1221320 1242366 1300455 1318416 1319376 1320504 1336379 1351335 1356389 1377479 1429498 1434519 1447461 1535483 1553399 1557471 1558575 1575566 1577006 1646650 1690477 1818611 
15.0 0.235 1.155 6.782 8.236 18.227 16.401 2.323 4.779 8.346 19.814 4.661 15.004 12.116 0.139 0.243 10.777 0.005 2.948 7.711 18.035 1.522 0.139 15.259 15.261 0.938 4.641 0.849 2.026 10.084 0.448 3.564 11.15 0.795 3.484 3.477 2.368 15.231 2.393 5.239 3.346 2.869 3.262 3.262 0.951 2.771 0.088 0.765 3.13 2.569 23.768 2.097 5.11 1.521 1.533 20.093 6.937 0.139 0.677 1.854 21.712 8.171 1.04 3.326 1.436 0.387 2.544 0.635 0.252 25.266 1.67 0.524 2.138 3.95 28.578 12.222 1.997 8.721 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:204
 Score: 88.805, AlignedPeaks: 1176488 1290626 1419789 1547789 1694761 
0 174027 207981 214268 242128 245355 257209 298667 300287 304374 316140 400208 409286 411297 413231 430180 446325 483412 522140 530675 543386 550454 559570 560375 561236 577348 588441 600920 620901 663296 671644 672471 680415 681910 690355 706627 708145 730442 765068 773969 802750 817468 818346 836616 846025 847464 860777 877370 895212 904079 947491 990469 1007537 1015082 1023680 1032059 1061553 1101491 1116749 1118544 1119532 1121397 1136655 1176488 1206087 1230544 1241810 1247675 1277079 1290626 1334067 1342934 1360768 1377369 1390682 1395535 1398664 1399403 1419789 1420678 1435396 1464177 1503430 1528153 1530001 1531519 1536764 1547789 1557731 1565675 1566502 1574850 1614191 1632000 1637226 1649705 1674529 1676910 1677771 1678575 1687692 1690607 1694761 1707471 1716006 1742885 1756786 1808053 1824915 1826849 1828860 1837263 1837938 1922080 1928773 1933772 1937859 1938823 1939479 1942864 1955046 1980936 1992712 2023878 2030164 2064118 2220135 
15.0 6.36 0.568 0.808 1.036 8.489 3.703 0.668 1.995 1.391 13.387 2.761 0.643 1.277 1.194 12.364 0.669 1.44 0.859 5.06 14.139 1.418 11.331 14.418 9.19 0.897 2.162 5.538 0.033 1.926 0.611 2.589 0.347 0.042 10.483 7.13 8.072 0.399 1.028 0.715 2.759 5.204 21.276 0.991 1.371 2.267 6.485 17.743 6.481 0.557 13.075 13.385 2.648 0.938 1.364 2.647 14.272 6.002 4.816 24.535 21.312 2.079 8.683 11.574 3.977 2.759 0.243 20.493 0.658 11.629 2.711 9.75 15.343 12.933 2.725 1.144 5.9 2.75 25.764 2.535 4.039 1.617 2.287 2.265 2.825 5.26 1.066 18.104 0.791 7.192 1.527 2.131 1.201 0.05 7.726 2.186 3.132 6.404 13.718 15.621 1.482 0.967 21.734 3.112 1.711 1.422 1.664 17.755 0.412 0.73 1.401 0.775 1.484 15.814 0.362 0.834 5.294 0.748 0.432 0.417 0.456 0.652 9.457 0.554 1.814 7.006 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_750_0.prm:22
 Score: 83.875, AlignedPeaks: 1230585 1344579 1473707 1601671 1748676 1877120 
0 173700 216859 239315 242241 257220 259957 281229 282078 288128 299113 300273 385168 386299 395526 401302 402242 402916 403562 413012 416055 419996 465328 514096 515354 516582 522212 538450 551611 572605 578179 586071 586918 615243 661206 662356 672142 693451 703334 708044 727959 742785 777891 788401 790301 791545 800222 806446 807516 808560 865723 874559 877214 901287 913295 919429 920622 930557 931365 936384 936996 954334 972291 988023 1033386 1043404 1044415 1045165 1050232 1050953 1061610 1077399 1090422 1091190 1119374 1144656 1172840 1173587 1190576 1205298 1213798 1218865 1219550 1220626 1230585 1276007 1327034 1332661 1333473 1342013 1343408 1344579 1350735 1362743 1386861 1389471 1398307 1456514 1457584 1462960 1463808 1472485 1473707 1475629 1486139 1520465 1521245 1591890 1601671 1602824 1620688 1648787 1677112 1677959 1685851 1691425 1712419 1725580 1741817 1747448 1748676 1749934 1765055 1786226 1798702 1847975 1851018 1855498 1860468 1861788 1862728 1868504 1877120 1877731 1878862 1883640 1963757 1964917 1975997 1982801 2004073 2006810 2021789 2047188 2090330 2101906 2117464 2246020 
15.0 2.259 7.764 0.265 1.501 0.404 4.028 0.013 0.029 17.526 1.908 3.297 0.576 0.702 0.839 4.276 15.526 3.813 13.693 2.059 0.948 5.131 2.979 7.586 7.619 4.574 1.26 0.343 1.052 1.801 1.583 1.205 1.161 2.571 4.237 10.901 4.468 0.695 0.943 1.702 0.476 0.348 8.654 2.515 16.571 7.416 1.549 3.721 8.143 3.613 1.764 0.648 5.364 2.346 1.771 14.574 4.844 7.301 10.631 0.627 2.898 2.198 0.34 1.189 11.14 2.166 10.605 1.244 2.633 2.576 2.684 2.896 13.491 12.26 6.64 5.739 6.345 16.358 5.038 0.923 2.224 2.242 15.394 3.949 11.741 0.743 1.85 16.662 12.321 3.341 6.003 19.197 2.51 4.319 5.016 0.479 1.225 8.161 4.142 1.386 0.611 10.735 22.454 2.346 4.854 2.913 3.662 6.795 15.015 1.807 2.184 1.708 2.876 1.604 2.453 2.15 2.022 1.014 0.736 4.34 14.376 9.838 0.413 2.699 1.645 2.209 0.797 0.528 8.867 16.996 0.369 0.184 1.092 0.998 0.841 0.382 1.578 3.124 11.912 1.322 2.012 1.101 0.381 8.787 2.51 1.854 5.817 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_675_0.prm:69
 Score: 78.92999999999999, AlignedPeaks: 0 259087 502249 777204 905227 
0 128372 129502 144007 162924 239081 241188 250831 251446 259087 259694 294116 340069 341823 342378 352349 387264 419286 466406 469327 490348 500273 502249 525186 553252 595356 597361 605245 640189 663199 695716 696328 704543 705365 711378 752099 777204 786247 795231 807187 807885 816644 821842 838457 874304 905227 923243 952319 954571 987313 1005511 1022278 1032175 1080496 1115501 1193779 1228433 1356567 
15.0 1.728 4.131 3.4 5.108 3.387 28.961 0.344 4.068 13.558 3.743 6.372 1.051 4.469 10.676 11.424 0.554 1.537 1.561 13.992 5.638 0.3 3.196 1.768 1.48 1.307 11.314 0.278 1.816 0.55 4.66 1.829 3.85 2.378 1.143 0.791 16.016 9.1 3.514 2.221 3.243 1.638 1.377 3.589 1.117 16.16 0.514 0.267 0.524 1.25 1.229 4.338 8.058 5.975 17.868 14.505 9.888 15.0 

SpectrumHMM Model: * M[0] - Mass:-71029.0 Overlap:2/4 LogOddsScore:2.3310755687248723, SumScore:17.982999999999997, InsertsAfter: 181
 * M[1] - Mass:-39811.0 Overlap:2/4 LogOddsScore:2.3310755687248723, SumScore:28.374, InsertsAfter: 9
 * M[2] - Mass:0.0 Overlap:4/6 LogOddsScore:4.139269014485919, SumScore:43.628, InsertsAfter: 11
 * M[3] - Mass:30436.0 Overlap:2/6 LogOddsScore:1.643215265355149, SumScore:14.026, InsertsAfter: 3
 * M[4] - Mass:73358.625 Overlap:3/6 LogOddsScore:2.891242139920534, SumScore:27.12, InsertsAfter: 8
 * M[5] - Mass:259411.33333333334 Overlap:5/6 LogOddsScore:7.808780741718402, SumScore:89.325, InsertsAfter: 44
 * M[6] - Mass:373414.0 Overlap:6/6 LogOddsScore:12.237705377192452, SumScore:143.47, InsertsAfter: 24
 * M[7] - Mass:502497.4166666666 Overlap:6/6 LogOddsScore:13.448447803526, SumScore:160.25400000000002, InsertsAfter: 34
 * M[8] - Mass:630610.3333333334 Overlap:5/6 LogOddsScore:10.989678502627067, SumScore:113.4935, InsertsAfter: 29
 * M[9] - Mass:777631.0 Overlap:5/6 LogOddsScore:9.01952316805195, SumScore:87.992, InsertsAfter: 39
 * M[10] - Mass:905592.8333333333 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:51.9315, InsertsAfter: 22
 * M[11] - Mass:963286.0 Overlap:1/5 LogOddsScore:-0.4716238838589232, SumScore:7.85, InsertsAfter: 13
 * M[12] - Mass:1090813.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 21
 * M[13] - Mass:1161613.75 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:52.5, InsertsAfter: 6
 * M[14] - Mass:1262897.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 0
ConsensusPRM: -71029 -39811 0 30436 73358 259411 373414 502497 630610 777631 905592 963286 1090813 1161613 1262897 Consensus: -71029 -39811 0 30436 73358 259411 373414 502497 630610 777631 905592 963286 1090813 1161613 1262897
De Novo: A[259.411]NEKFQ[185.221]AT, Merged: IWNEKFQGKATFTADTSSN
-71029 -39811 0 30436 73358 259411 373414 502497 630610 777631 905592 962719 963286 1090813 1161613 1262897 1409965 1511012 1582049 1697075 1798122 1885154 1972186 2086228 
17.982999999999997 28.374 32.721000000000004 14.026 27.12 67.62100000000001 103.7085 112.542 82.645 65.039 44.620999999999995 30.0 7.85 30.0 45.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 

(LEFT)Round: 2 for seed: IWNEKFQGKATFTADTSSN
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:204
 Score: 119.93299999999999, AlignedPeaks: 877370 990469 1176488 1290626 1419789 1547789 1694761 
0 174027 207981 214268 242128 245355 257209 298667 300287 304374 316140 400208 409286 411297 413231 430180 446325 483412 522140 530675 543386 550454 559570 560375 561236 577348 588441 600920 620901 663296 671644 672471 680415 681910 690355 706627 708145 730442 765068 773969 802750 817468 818346 836616 846025 847464 860777 877370 895212 904079 947491 990469 1007537 1015082 1023680 1032059 1061553 1101491 1116749 1118544 1119532 1121397 1136655 1176488 1206087 1230544 1241810 1247675 1277079 1290626 1334067 1342934 1360768 1377369 1390682 1395535 1398664 1399403 1419789 1420678 1435396 1464177 1503430 1528153 1530001 1531519 1536764 1547789 1557731 1565675 1566502 1574850 1614191 1632000 1637226 1649705 1674529 1676910 1677771 1678575 1687692 1690607 1694761 1707471 1716006 1742885 1756786 1808053 1824915 1826849 1828860 1837263 1837938 1922080 1928773 1933772 1937859 1938823 1939479 1942864 1955046 1980936 1992712 2023878 2030164 2064118 2220135 
15.0 6.36 0.568 0.808 1.036 8.489 3.703 0.668 1.995 1.391 13.387 2.761 0.643 1.277 1.194 12.364 0.669 1.44 0.859 5.06 14.139 1.418 11.331 14.418 9.19 0.897 2.162 5.538 0.033 1.926 0.611 2.589 0.347 0.042 10.483 7.13 8.072 0.399 1.028 0.715 2.759 5.204 21.276 0.991 1.371 2.267 6.485 17.743 6.481 0.557 13.075 13.385 2.648 0.938 1.364 2.647 14.272 6.002 4.816 24.535 21.312 2.079 8.683 11.574 3.977 2.759 0.243 20.493 0.658 11.629 2.711 9.75 15.343 12.933 2.725 1.144 5.9 2.75 25.764 2.535 4.039 1.617 2.287 2.265 2.825 5.26 1.066 18.104 0.791 7.192 1.527 2.131 1.201 0.05 7.726 2.186 3.132 6.404 13.718 15.621 1.482 0.967 21.734 3.112 1.711 1.422 1.664 17.755 0.412 0.73 1.401 0.775 1.484 15.814 0.362 0.834 5.294 0.748 0.432 0.417 0.456 0.652 9.457 0.554 1.814 7.006 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_750_0.prm:22
 Score: 105.11100000000002, AlignedPeaks: 931365 1044415 1230585 1344579 1473707 1601671 1748676 1877120 
0 173700 216859 239315 242241 257220 259957 281229 282078 288128 299113 300273 385168 386299 395526 401302 402242 402916 403562 413012 416055 419996 465328 514096 515354 516582 522212 538450 551611 572605 578179 586071 586918 615243 661206 662356 672142 693451 703334 708044 727959 742785 777891 788401 790301 791545 800222 806446 807516 808560 865723 874559 877214 901287 913295 919429 920622 930557 931365 936384 936996 954334 972291 988023 1033386 1043404 1044415 1045165 1050232 1050953 1061610 1077399 1090422 1091190 1119374 1144656 1172840 1173587 1190576 1205298 1213798 1218865 1219550 1220626 1230585 1276007 1327034 1332661 1333473 1342013 1343408 1344579 1350735 1362743 1386861 1389471 1398307 1456514 1457584 1462960 1463808 1472485 1473707 1475629 1486139 1520465 1521245 1591890 1601671 1602824 1620688 1648787 1677112 1677959 1685851 1691425 1712419 1725580 1741817 1747448 1748676 1749934 1765055 1786226 1798702 1847975 1851018 1855498 1860468 1861788 1862728 1868504 1877120 1877731 1878862 1883640 1963757 1964917 1975997 1982801 2004073 2006810 2021789 2047188 2090330 2101906 2117464 2246020 
15.0 2.259 7.764 0.265 1.501 0.404 4.028 0.013 0.029 17.526 1.908 3.297 0.576 0.702 0.839 4.276 15.526 3.813 13.693 2.059 0.948 5.131 2.979 7.586 7.619 4.574 1.26 0.343 1.052 1.801 1.583 1.205 1.161 2.571 4.237 10.901 4.468 0.695 0.943 1.702 0.476 0.348 8.654 2.515 16.571 7.416 1.549 3.721 8.143 3.613 1.764 0.648 5.364 2.346 1.771 14.574 4.844 7.301 10.631 0.627 2.898 2.198 0.34 1.189 11.14 2.166 10.605 1.244 2.633 2.576 2.684 2.896 13.491 12.26 6.64 5.739 6.345 16.358 5.038 0.923 2.224 2.242 15.394 3.949 11.741 0.743 1.85 16.662 12.321 3.341 6.003 19.197 2.51 4.319 5.016 0.479 1.225 8.161 4.142 1.386 0.611 10.735 22.454 2.346 4.854 2.913 3.662 6.795 15.015 1.807 2.184 1.708 2.876 1.604 2.453 2.15 2.022 1.014 0.736 4.34 14.376 9.838 0.413 2.699 1.645 2.209 0.797 0.528 8.867 16.996 0.369 0.184 1.092 0.998 0.841 0.382 1.578 3.124 11.912 1.322 2.012 1.101 0.381 8.787 2.51 1.854 5.817 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:96
 Score: 99.795, AlignedPeaks: 877358 990366 1176468 1290450 1419490 1547531 1694611 
0 129070 160362 214313 225198 229664 231165 242067 243086 300166 301575 302274 399251 402224 402848 415722 416264 432664 438858 469162 481148 514982 523753 526390 529268 543505 544242 545874 559906 616934 643280 645228 660146 664721 675790 676347 679979 687363 693204 715731 717007 758159 765433 802276 804398 821072 822346 828295 847966 876268 877358 895607 933459 950482 961152 977091 990366 990846 1005284 1007362 1008127 1031758 1047407 1087382 1104446 1119440 1136497 1176468 1192121 1215752 1216517 1233032 1233502 1262727 1273397 1290450 1306425 1319801 1328272 1346521 1347611 1375913 1376608 1401533 1402807 1419490 1458446 1493606 1493860 1513952 1530675 1543900 1547531 1548088 1550350 1559158 1563733 1578651 1580599 1606945 1615685 1635406 1663973 1671412 1678002 1679639 1680374 1694611 1697489 1700126 1707072 1708896 1742731 1785021 1807615 1808156 1821031 1821655 1830265 1921605 1922304 1923713 1924538 1966703 1980792 1981812 1992709 2009566 2063516 2205868 
15.0 2.217 6.79 1.009 0.017 1.21 10.946 1.256 7.616 2.662 7.493 12.621 0.007 0.443 0.767 5.027 13.159 1.07 1.113 1.514 1.84 2.056 1.367 1.935 7.963 0.927 4.367 11.023 0.868 1.535 3.588 0.736 1.227 1.716 4.404 10.768 1.169 0.099 4.459 0.135 0.578 1.26 0.165 2.417 18.507 1.595 1.047 0.846 0.205 3.973 6.518 0.822 10.073 0.797 0.154 0.44 15.307 13.752 1.842 5.838 2.634 1.48 13.04 2.481 20.374 17.627 5.412 13.666 2.782 3.144 4.942 18.042 22.871 0.984 1.746 10.87 0.789 2.295 2.363 12.102 2.044 0.36 0.684 1.547 4.227 23.723 0.814 1.46 1.754 0.746 3.771 0.07 16.695 4.34 0.559 0.822 3.69 1.786 4.227 1.548 0.002 1.512 3.041 0.878 10.425 5.317 1.527 13.016 2.961 0.989 0.357 4.207 0.737 0.963 17.162 0.992 1.487 1.361 0.298 11.109 4.855 3.958 1.116 0.132 2.469 0.66 10.339 0.266 6.808 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:387
 Score: 98.779, AlignedPeaks: 1018352 1204378 1318416 1447461 1575566 
0 103009 189972 199993 259615 261089 278047 279150 300644 301139 389198 401262 402102 407123 419042 423128 459144 485286 516116 517245 518236 536166 594255 630213 632256 648181 650190 666118 668212 717287 762258 774277 779273 795232 797284 815256 832201 861248 878243 935549 935986 936298 944557 944860 975371 991593 993365 1000667 1018352 1027071 1057339 1068721 1119353 1122267 1155405 1204378 1206429 1221320 1242366 1300455 1318416 1319376 1320504 1336379 1351335 1356389 1377479 1429498 1434519 1447461 1535483 1553399 1557471 1558575 1575566 1577006 1646650 1690477 1818611 
15.0 0.235 1.155 6.782 8.236 18.227 16.401 2.323 4.779 8.346 19.814 4.661 15.004 12.116 0.139 0.243 10.777 0.005 2.948 7.711 18.035 1.522 0.139 15.259 15.261 0.938 4.641 0.849 2.026 10.084 0.448 3.564 11.15 0.795 3.484 3.477 2.368 15.231 2.393 5.239 3.346 2.869 3.262 3.262 0.951 2.771 0.088 0.765 3.13 2.569 23.768 2.097 5.11 1.521 1.533 20.093 6.937 0.139 0.677 1.854 21.712 8.171 1.04 3.326 1.436 0.387 2.544 0.635 0.252 25.266 1.67 0.524 2.138 3.95 28.578 12.222 1.997 8.721 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:291
 Score: 78.31700000000001, AlignedPeaks: 489120 675133 789383 918431 1046494 
0 147176 242189 242995 275111 389390 390193 445877 476246 489120 541032 543969 549851 553880 575337 588290 674295 675133 675918 691343 693248 709417 722340 789383 790437 806327 807308 821513 917329 918431 1046494 
15.0 13.738 0.753 0.13 13.935 12.28 20.947 2.587 8.353 14.805 0.114 0.332 1.555 0.838 5.621 3.428 16.661 12.345 0.42 4.068 0.847 0.231 1.062 11.678 1.306 0.3 2.446 10.142 12.035 9.489 15.0 

SpectrumHMM Model: * M[0] - Mass:-877364.0 Overlap:2/4 LogOddsScore:3.541817995058421, SumScore:30.0, InsertsAfter: 2
 * M[1] - Mass:-316128.0 Overlap:2/5 LogOddsScore:0.7764029907064618, SumScore:11.761, InsertsAfter: 105
 * M[2] - Mass:-72971.0 Overlap:2/5 LogOddsScore:1.9871454170400107, SumScore:20.875, InsertsAfter: 65
 * M[3] - Mass:0.0 Overlap:5/7 LogOddsScore:7.4648505900335405, SumScore:63.266, InsertsAfter: 21
 * M[4] - Mass:113086.40000000001 Overlap:7/7 LogOddsScore:12.382389191831408, SumScore:84.352, InsertsAfter: 28
 * M[5] - Mass:299109.19999999995 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:141.356, InsertsAfter: 50
 * M[6] - Mass:413218.6 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:178.7945, InsertsAfter: 28
 * M[7] - Mass:542318.9333333332 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:219.238, InsertsAfter: 40
 * M[8] - Mass:670343.2666666667 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:176.037, InsertsAfter: 23
 * M[9] - Mass:817334.0833333333 Overlap:5/6 LogOddsScore:10.736540866546544, SumScore:114.165, InsertsAfter: 42
 * M[10] - Mass:945684.6 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:45.712999999999994, InsertsAfter: 27
 * M[11] - Mass:1002530.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 9
 * M[12] - Mass:1130624.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 26
 * M[13] - Mass:1201424.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:45.0, InsertsAfter: 8
ConsensusPRM: -877364 -316128 -72971 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 Consensus: -877364 -316128 -72971 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424
De Novo: [316.128]IWNEQFKGKA, Merged: [316.128]IWNEQFKGKATFTADTSSN
-877364 -316128 -72971 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 1302708 1449776 1550823 1621860 1736886 1837933 1924965 2011997 2126039 
30.0 11.761 20.875 45.82 55.736000000000004 104.4885 141.2515 165.89 129.341 89.602 45.166999999999994 30.0 30.0 45.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 

(LEFT)Round: 3 for seed: [316.128]IWNEQFKGKATFTADTSSN
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:204
 Score: 129.123, AlignedPeaks: 561236 877370 990469 1176488 1290626 1419789 1547789 1694761 
0 174027 207981 214268 242128 245355 257209 298667 300287 304374 316140 400208 409286 411297 413231 430180 446325 483412 522140 530675 543386 550454 559570 560375 561236 577348 588441 600920 620901 663296 671644 672471 680415 681910 690355 706627 708145 730442 765068 773969 802750 817468 818346 836616 846025 847464 860777 877370 895212 904079 947491 990469 1007537 1015082 1023680 1032059 1061553 1101491 1116749 1118544 1119532 1121397 1136655 1176488 1206087 1230544 1241810 1247675 1277079 1290626 1334067 1342934 1360768 1377369 1390682 1395535 1398664 1399403 1419789 1420678 1435396 1464177 1503430 1528153 1530001 1531519 1536764 1547789 1557731 1565675 1566502 1574850 1614191 1632000 1637226 1649705 1674529 1676910 1677771 1678575 1687692 1690607 1694761 1707471 1716006 1742885 1756786 1808053 1824915 1826849 1828860 1837263 1837938 1922080 1928773 1933772 1937859 1938823 1939479 1942864 1955046 1980936 1992712 2023878 2030164 2064118 2220135 
15.0 6.36 0.568 0.808 1.036 8.489 3.703 0.668 1.995 1.391 13.387 2.761 0.643 1.277 1.194 12.364 0.669 1.44 0.859 5.06 14.139 1.418 11.331 14.418 9.19 0.897 2.162 5.538 0.033 1.926 0.611 2.589 0.347 0.042 10.483 7.13 8.072 0.399 1.028 0.715 2.759 5.204 21.276 0.991 1.371 2.267 6.485 17.743 6.481 0.557 13.075 13.385 2.648 0.938 1.364 2.647 14.272 6.002 4.816 24.535 21.312 2.079 8.683 11.574 3.977 2.759 0.243 20.493 0.658 11.629 2.711 9.75 15.343 12.933 2.725 1.144 5.9 2.75 25.764 2.535 4.039 1.617 2.287 2.265 2.825 5.26 1.066 18.104 0.791 7.192 1.527 2.131 1.201 0.05 7.726 2.186 3.132 6.404 13.718 15.621 1.482 0.967 21.734 3.112 1.711 1.422 1.664 17.755 0.412 0.73 1.401 0.775 1.484 15.814 0.362 0.834 5.294 0.748 0.432 0.417 0.456 0.652 9.457 0.554 1.814 7.006 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_750_0.prm:22
 Score: 107.68200000000002, AlignedPeaks: 615243 931365 1044415 1230585 1344579 1473707 1601671 1748676 1877120 
0 173700 216859 239315 242241 257220 259957 281229 282078 288128 299113 300273 385168 386299 395526 401302 402242 402916 403562 413012 416055 419996 465328 514096 515354 516582 522212 538450 551611 572605 578179 586071 586918 615243 661206 662356 672142 693451 703334 708044 727959 742785 777891 788401 790301 791545 800222 806446 807516 808560 865723 874559 877214 901287 913295 919429 920622 930557 931365 936384 936996 954334 972291 988023 1033386 1043404 1044415 1045165 1050232 1050953 1061610 1077399 1090422 1091190 1119374 1144656 1172840 1173587 1190576 1205298 1213798 1218865 1219550 1220626 1230585 1276007 1327034 1332661 1333473 1342013 1343408 1344579 1350735 1362743 1386861 1389471 1398307 1456514 1457584 1462960 1463808 1472485 1473707 1475629 1486139 1520465 1521245 1591890 1601671 1602824 1620688 1648787 1677112 1677959 1685851 1691425 1712419 1725580 1741817 1747448 1748676 1749934 1765055 1786226 1798702 1847975 1851018 1855498 1860468 1861788 1862728 1868504 1877120 1877731 1878862 1883640 1963757 1964917 1975997 1982801 2004073 2006810 2021789 2047188 2090330 2101906 2117464 2246020 
15.0 2.259 7.764 0.265 1.501 0.404 4.028 0.013 0.029 17.526 1.908 3.297 0.576 0.702 0.839 4.276 15.526 3.813 13.693 2.059 0.948 5.131 2.979 7.586 7.619 4.574 1.26 0.343 1.052 1.801 1.583 1.205 1.161 2.571 4.237 10.901 4.468 0.695 0.943 1.702 0.476 0.348 8.654 2.515 16.571 7.416 1.549 3.721 8.143 3.613 1.764 0.648 5.364 2.346 1.771 14.574 4.844 7.301 10.631 0.627 2.898 2.198 0.34 1.189 11.14 2.166 10.605 1.244 2.633 2.576 2.684 2.896 13.491 12.26 6.64 5.739 6.345 16.358 5.038 0.923 2.224 2.242 15.394 3.949 11.741 0.743 1.85 16.662 12.321 3.341 6.003 19.197 2.51 4.319 5.016 0.479 1.225 8.161 4.142 1.386 0.611 10.735 22.454 2.346 4.854 2.913 3.662 6.795 15.015 1.807 2.184 1.708 2.876 1.604 2.453 2.15 2.022 1.014 0.736 4.34 14.376 9.838 0.413 2.699 1.645 2.209 0.797 0.528 8.867 16.996 0.369 0.184 1.092 0.998 0.841 0.382 1.578 3.124 11.912 1.322 2.012 1.101 0.381 8.787 2.51 1.854 5.817 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:96
 Score: 99.795, AlignedPeaks: 877358 990366 1176468 1290450 1419490 1547531 1694611 
0 129070 160362 214313 225198 229664 231165 242067 243086 300166 301575 302274 399251 402224 402848 415722 416264 432664 438858 469162 481148 514982 523753 526390 529268 543505 544242 545874 559906 616934 643280 645228 660146 664721 675790 676347 679979 687363 693204 715731 717007 758159 765433 802276 804398 821072 822346 828295 847966 876268 877358 895607 933459 950482 961152 977091 990366 990846 1005284 1007362 1008127 1031758 1047407 1087382 1104446 1119440 1136497 1176468 1192121 1215752 1216517 1233032 1233502 1262727 1273397 1290450 1306425 1319801 1328272 1346521 1347611 1375913 1376608 1401533 1402807 1419490 1458446 1493606 1493860 1513952 1530675 1543900 1547531 1548088 1550350 1559158 1563733 1578651 1580599 1606945 1615685 1635406 1663973 1671412 1678002 1679639 1680374 1694611 1697489 1700126 1707072 1708896 1742731 1785021 1807615 1808156 1821031 1821655 1830265 1921605 1922304 1923713 1924538 1966703 1980792 1981812 1992709 2009566 2063516 2205868 
15.0 2.217 6.79 1.009 0.017 1.21 10.946 1.256 7.616 2.662 7.493 12.621 0.007 0.443 0.767 5.027 13.159 1.07 1.113 1.514 1.84 2.056 1.367 1.935 7.963 0.927 4.367 11.023 0.868 1.535 3.588 0.736 1.227 1.716 4.404 10.768 1.169 0.099 4.459 0.135 0.578 1.26 0.165 2.417 18.507 1.595 1.047 0.846 0.205 3.973 6.518 0.822 10.073 0.797 0.154 0.44 15.307 13.752 1.842 5.838 2.634 1.48 13.04 2.481 20.374 17.627 5.412 13.666 2.782 3.144 4.942 18.042 22.871 0.984 1.746 10.87 0.789 2.295 2.363 12.102 2.044 0.36 0.684 1.547 4.227 23.723 0.814 1.46 1.754 0.746 3.771 0.07 16.695 4.34 0.559 0.822 3.69 1.786 4.227 1.548 0.002 1.512 3.041 0.878 10.425 5.317 1.527 13.016 2.961 0.989 0.357 4.207 0.737 0.963 17.162 0.992 1.487 1.361 0.298 11.109 4.855 3.958 1.116 0.132 2.469 0.66 10.339 0.266 6.808 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:387
 Score: 98.779, AlignedPeaks: 1018352 1204378 1318416 1447461 1575566 
0 103009 189972 199993 259615 261089 278047 279150 300644 301139 389198 401262 402102 407123 419042 423128 459144 485286 516116 517245 518236 536166 594255 630213 632256 648181 650190 666118 668212 717287 762258 774277 779273 795232 797284 815256 832201 861248 878243 935549 935986 936298 944557 944860 975371 991593 993365 1000667 1018352 1027071 1057339 1068721 1119353 1122267 1155405 1204378 1206429 1221320 1242366 1300455 1318416 1319376 1320504 1336379 1351335 1356389 1377479 1429498 1434519 1447461 1535483 1553399 1557471 1558575 1575566 1577006 1646650 1690477 1818611 
15.0 0.235 1.155 6.782 8.236 18.227 16.401 2.323 4.779 8.346 19.814 4.661 15.004 12.116 0.139 0.243 10.777 0.005 2.948 7.711 18.035 1.522 0.139 15.259 15.261 0.938 4.641 0.849 2.026 10.084 0.448 3.564 11.15 0.795 3.484 3.477 2.368 15.231 2.393 5.239 3.346 2.869 3.262 3.262 0.951 2.771 0.088 0.765 3.13 2.569 23.768 2.097 5.11 1.521 1.533 20.093 6.937 0.139 0.677 1.854 21.712 8.171 1.04 3.326 1.436 0.387 2.544 0.635 0.252 25.266 1.67 0.524 2.138 3.95 28.578 12.222 1.997 8.721 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:291
 Score: 78.31700000000001, AlignedPeaks: 489120 675133 789383 918431 1046494 
0 147176 242189 242995 275111 389390 390193 445877 476246 489120 541032 543969 549851 553880 575337 588290 674295 675133 675918 691343 693248 709417 722340 789383 790437 806327 807308 821513 917329 918431 1046494 
15.0 13.738 0.753 0.13 13.935 12.28 20.947 2.587 8.353 14.805 0.114 0.332 1.555 0.838 5.621 3.428 16.661 12.345 0.42 4.068 0.847 0.231 1.062 11.678 1.306 0.3 2.446 10.142 12.035 9.489 15.0 

SpectrumHMM Model: * M[0] - Mass:-561233.0 Overlap:2/4 LogOddsScore:3.541817995058421, SumScore:30.0, InsertsAfter: 2
 * M[1] - Mass:-369.0 Overlap:4/7 LogOddsScore:3.7953388628010574, SumScore:28.75, InsertsAfter: 104
 * M[2] - Mass:243115.5 Overlap:2/7 LogOddsScore:1.2992851136702874, SumScore:20.875, InsertsAfter: 66
 * M[3] - Mass:316128.0 Overlap:5/7 LogOddsScore:7.4648505900335405, SumScore:80.712, InsertsAfter: 21
 * M[4] - Mass:429190.6923076923 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:112.96800000000002, InsertsAfter: 28
 * M[5] - Mass:615264.6153846154 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:173.9075, InsertsAfter: 51
 * M[6] - Mass:729324.3846153846 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:216.33749999999998, InsertsAfter: 27
 * M[7] - Mass:858419.0769230769 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:272.586, InsertsAfter: 40
 * M[8] - Mass:986443.1538461539 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:222.73299999999998, InsertsAfter: 23
 * M[9] - Mass:1133447.9000000001 Overlap:5/6 LogOddsScore:10.736540866546544, SumScore:138.728, InsertsAfter: 42
 * M[10] - Mass:1261860.75 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:46.25899999999999, InsertsAfter: 27
 * M[11] - Mass:1318658.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 9
 * M[12] - Mass:1446752.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 26
ConsensusPRM: -561233 -369 243115 316128 429190 615264 729324 858419 986443 1133447 1261860 1318658 1446752 Consensus: -561233 -369 243115 316128 429190 615264 729324 858419 986443 1133447 1261860 1318658 1446752
De Novo: [316.497]IWNEQFKGK, Merged: [316.497]IWNEQFKGKATFTADTSSN
-561233 -369 243115 316128 429190 615264 729324 858419 986443 1133447 1261860 1318658 1446752 1517552 1618836 1765904 1866951 1937988 2053014 2154061 2241093 2328125 2442167 
30.0 20.255499999999998 20.875 63.266000000000005 84.352 139.198 178.79449999999997 219.238 176.03699999999998 114.165 45.712999999999994 30.0 30.0 45.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 
(RIGHT)Round: 0 for seed: [316.128]IWNEQFKGKATFTADTSSN
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_850_0.prm:57
 Score: 106.614, AlignedPeaks: 0 172052 319198 420170 491101 606272 707247 995357 
0 172052 231767 241231 248112 248534 258016 259149 276113 277083 295001 319198 337010 361161 371163 372130 389186 390198 407392 420170 422041 431137 448363 475042 491101 535131 535799 553226 578100 605567 606272 622305 624154 682424 690267 707247 717486 725232 734235 740650 743784 750267 781514 795219 821282 839434 853301 855789 873835 876323 882146 882880 891601 908379 930454 939162 948110 985877 994314 995357 1003094 1022366 1039356 1047199 1050946 1059704 1068650 1123363 1124057 1132298 1141349 1151524 1153354 1184857 1193825 1194478 1229450 1238564 1254581 1256564 1279382 1281260 1298486 1309445 1322232 1325559 1339426 1340438 1357503 1410426 1427959 1452541 1453494 1470485 1471608 1481089 1481511 1497856 1557572 1711613 
15.0 0.519 1.277 12.002 2.424 2.423 11.121 30.209 20.737 15.039 2.804 10.004 1.766 0.101 1.61 33.543 10.959 14.825 1.491 6.687 0.536 0.233 0.159 0.334 11.868 20.943 1.701 2.718 0.534 1.154 20.283 1.117 0.866 0.431 0.579 13.772 0.72 0.235 12.973 1.525 3.419 1.933 0.015 2.961 12.872 0.213 0.023 0.543 0.519 0.318 2.784 3.378 2.072 11.272 5.953 5.045 1.26 8.825 6.999 13.481 4.947 10.473 0.942 0.61 5.248 3.882 0.843 14.393 1.203 1.681 0.319 2.296 1.168 0.069 0.272 13.656 0.86 7.562 1.658 2.19 0.278 0.544 0.592 4.317 0.439 5.11 1.785 4.746 34.822 8.355 0.549 8.084 8.988 32.059 5.442 3.193 3.736 3.52 1.82 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:235
 Score: 93.369, AlignedPeaks: 0 186223 287190 374198 
0 147090 186223 276152 287190 305217 374198 377118 377590 433966 434219 489173 499117 538983 547586 548261 556694 560506 571211 603642 608157 612376 626182 626435 682811 683248 686183 704274 766567 773209 784251 801289 874242 913311 1042391 
15.0 12.671 10.96 0.659 32.153 6.958 20.256 4.954 5.167 1.135 2.529 6.225 0.376 7.229 4.389 4.308 1.348 1.727 3.692 1.43 0.511 3.169 1.388 0.997 4.635 3.218 8.749 1.587 0.975 12.669 7.855 0.504 8.653 15.154 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_575_0.prm:503
 Score: 92.22200000000001, AlignedPeaks: 0 186142 287174 374198 
0 186142 261113 287174 305225 374198 390190 392231 419156 443741 482105 489211 491200 506004 547853 556775 579318 595651 596098 604535 605012 605325 613760 617669 626592 653252 685257 692339 730703 737358 739826 748476 782213 784269 797330 800246 818334 832363 887250 895501 904273 913308 931244 1025273 1042310 1156434 
15.0 1.534 9.801 41.45 5.33 19.238 6.58 0.114 1.24 0.244 0.291 10.616 4.286 0.413 0.506 0.48 1.438 8.41 8.07 2.867 4.631 0.897 2.397 0.144 0.69 2.629 7.646 2.167 0.055 0.196 3.581 0.933 0.19 6.753 0.724 9.301 4.14 1.231 13.607 0.851 1.493 12.537 0.51 11.61 15.319 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:77
 Score: 91.94900000000001, AlignedPeaks: 0 318924 434177 535193 622096 
0 248500 250724 298429 301129 318924 326165 335089 351201 352507 363185 370277 388246 396928 405975 421240 434177 434778 439252 447439 448161 452268 464788 466242 482865 501002 528186 535193 552720 561050 561910 562351 622096 639283 640063 649325 666351 717317 732863 735233 735987 737481 752055 763919 793810 850428 861206 863337 870537 879522 881435 951424 964466 976398 994482 1022367 1098235 1098962 1107444 1139400 1154050 1163114 1185357 1197324 1198058 1206323 1210978 1257432 1282269 1298438 1304632 1311343 1313777 1375773 1409736 1414959 1419592 1424309 1425803 1426562 1462391 1512422 1522508 1539704 1549641 1567629 1594386 1599476 1600048 1600740 1609071 1609769 1626598 1633604 1660788 1697002 1713643 1714351 1727012 1727678 1773544 1826726 1842866 1860661 1913291 2143780 
15.0 1.922 4.934 0.704 1.756 8.624 2.896 11.19 5.395 9.85 2.062 1.46 3.773 1.818 5.218 0.773 18.448 16.962 4.456 8.436 13.885 2.091 9.177 8.08 1.682 0.655 0.987 14.95 0.922 1.219 6.139 6.181 19.927 0.461 1.943 6.825 0.699 0.639 1.028 22.957 4.901 0.504 2.118 0.519 0.999 6.767 1.843 22.941 2.045 2.599 1.068 3.166 0.089 14.231 0.963 7.177 3.902 2.393 2.661 10.51 1.901 3.114 15.319 2.836 2.751 3.3 3.446 2.698 1.061 19.07 1.534 6.545 2.96 1.039 1.043 1.285 0.746 1.866 5.712 15.783 0.866 6.002 0.519 13.638 3.068 0.028 0.706 3.958 4.045 1.379 1.132 0.949 7.269 2.527 1.134 0.492 17.213 1.787 8.7 11.371 1.353 15.044 0.724 2.117 1.904 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_475_0.prm:134
 Score: 74.70400000000001, AlignedPeaks: 0 186121 287097 374322 575232 
0 186121 287097 308503 326504 374322 382710 393742 400150 415649 469398 496747 500110 502738 505994 508683 509848 519361 523523 537071 575232 580786 593419 626259 631989 688344 730095 789341 829082 957420 
15.0 21.962 13.428 1.651 0.211 1.519 1.598 3.311 19.041 2.69 2.365 7.206 0.097 3.269 8.487 1.565 1.233 0.433 4.281 0.163 7.795 3.448 3.108 0.008 0.668 12.757 6.071 16.191 8.098 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
 * M[1] - Mass:70800.0 Overlap:2/3 LogOddsScore:3.885748146743283, SumScore:45.0, InsertsAfter: 0
 * M[2] - Mass:172067.99999999997 Overlap:4/4 LogOddsScore:7.24861417052274, SumScore:45.519, InsertsAfter: 9
 * M[3] - Mass:319188.8 Overlap:3/4 LogOddsScore:4.789844869623806, SumScore:40.004, InsertsAfter: 7
 * M[4] - Mass:420263.9375 Overlap:6/6 LogOddsScore:10.267550042617335, SumScore:68.609, InsertsAfter: 7
 * M[5] - Mass:491083.0 Overlap:4/6 LogOddsScore:5.350011440819468, SumScore:50.492000000000004, InsertsAfter: 16
 * M[6] - Mass:606321.4375 Overlap:6/6 LogOddsScore:11.478292468950885, SumScore:101.653, InsertsAfter: 15
 * M[7] - Mass:707313.8750000001 Overlap:6/6 LogOddsScore:12.942172531364955, SumScore:104.303, InsertsAfter: 14
 * M[8] - Mass:794573.8124999998 Overlap:6/6 LogOddsScore:10.267550042617335, SumScore:74.66300000000001, InsertsAfter: 18
 * M[9] - Mass:881991.3999999999 Overlap:1/6 LogOddsScore:-0.815554035543785, SumScore:2.784, InsertsAfter: 34
 * M[10] - Mass:995386.4285714286 Overlap:4/6 LogOddsScore:6.560753867153017, SumScore:51.276, InsertsAfter: 41
 * M[11] - Mass:1194253.2 Overlap:3/4 LogOddsScore:3.5791024432902576, SumScore:33.502, InsertsAfter: 24
 * M[12] - Mass:1357472.0000000002 Overlap:2/4 LogOddsScore:3.794955631138943, SumScore:50.141000000000005, InsertsAfter: 11
 * M[13] - Mass:1462563.0 Overlap:1/3 LogOddsScore:1.4269788458443489, SumScore:15.0, InsertsAfter: 0
 * M[14] - Mass:1470503.5 Overlap:2/2 LogOddsScore:4.4828159345086664, SumScore:51.129, InsertsAfter: 18
 * M[15] - Mass:1711700.5 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:28.637999999999998, InsertsAfter: 22
ConsensusPRM: 0 70800 172067 319188 420263 491083 606321 707313 794573 881991 995386 1194253 1357472 1462563 1470503 1711700 Consensus: 0 70800 172067 319188 420263 491083 606321 707313 794573 881991 995386 1194253 1357472 1462563 1470503 1711700
De Novo: ATFTADTS[200.813][198.867]YI[241.197], Merged: [316.128]IWNEQFKGKATFTADTSSN[198.867]YI[241.197]
-316128 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 1302708 1449776 1550823 1621860 1736886 1837933 1924965 2011997 2012644 2126039 2324906 2488125 2593216 2601156 2842353 
11.761 45.82 55.736000000000004 104.4885 141.2515 165.89 129.341 89.602 45.166999999999994 30.0 37.5 43.331566872949296 37.7595 33.33356687294929 49.3045 36.90913374589859 65.82650000000001 67.1515 52.331500000000005 30.0 -13.90033127050705 37.301133745898596 30.165133745898594 43.46726749179719 8.32626749179718 51.129 28.637999999999998 
(RIGHT)Round: 1 for seed: [316.128]IWNEQFKGKATFTADTSSN[198.867]YI[241.197]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_850_0.prm:57
 Score: 176.628, AlignedPeaks: 420170 491101 606272 707247 995357 1194478 1357503 1470485 1711613 
0 172052 231767 241231 248112 248534 258016 259149 276113 277083 295001 319198 337010 361161 371163 372130 389186 390198 407392 420170 422041 431137 448363 475042 491101 535131 535799 553226 578100 605567 606272 622305 624154 682424 690267 707247 717486 725232 734235 740650 743784 750267 781514 795219 821282 839434 853301 855789 873835 876323 882146 882880 891601 908379 930454 939162 948110 985877 994314 995357 1003094 1022366 1039356 1047199 1050946 1059704 1068650 1123363 1124057 1132298 1141349 1151524 1153354 1184857 1193825 1194478 1229450 1238564 1254581 1256564 1279382 1281260 1298486 1309445 1322232 1325559 1339426 1340438 1357503 1410426 1427959 1452541 1453494 1470485 1471608 1481089 1481511 1497856 1557572 1711613 
15.0 0.519 1.277 12.002 2.424 2.423 11.121 30.209 20.737 15.039 2.804 10.004 1.766 0.101 1.61 33.543 10.959 14.825 1.491 6.687 0.536 0.233 0.159 0.334 11.868 20.943 1.701 2.718 0.534 1.154 20.283 1.117 0.866 0.431 0.579 13.772 0.72 0.235 12.973 1.525 3.419 1.933 0.015 2.961 12.872 0.213 0.023 0.543 0.519 0.318 2.784 3.378 2.072 11.272 5.953 5.045 1.26 8.825 6.999 13.481 4.947 10.473 0.942 0.61 5.248 3.882 0.843 14.393 1.203 1.681 0.319 2.296 1.168 0.069 0.272 13.656 0.86 7.562 1.658 2.19 0.278 0.544 0.592 4.317 0.439 5.11 1.785 4.746 34.822 8.355 0.549 8.084 8.988 32.059 5.442 3.193 3.736 3.52 1.82 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:77
 Score: 117.15300000000002, AlignedPeaks: 318924 434177 535193 622096 1022367 1185357 1298438 1539704 
0 248500 250724 298429 301129 318924 326165 335089 351201 352507 363185 370277 388246 396928 405975 421240 434177 434778 439252 447439 448161 452268 464788 466242 482865 501002 528186 535193 552720 561050 561910 562351 622096 639283 640063 649325 666351 717317 732863 735233 735987 737481 752055 763919 793810 850428 861206 863337 870537 879522 881435 951424 964466 976398 994482 1022367 1098235 1098962 1107444 1139400 1154050 1163114 1185357 1197324 1198058 1206323 1210978 1257432 1282269 1298438 1304632 1311343 1313777 1375773 1409736 1414959 1419592 1424309 1425803 1426562 1462391 1512422 1522508 1539704 1549641 1567629 1594386 1599476 1600048 1600740 1609071 1609769 1626598 1633604 1660788 1697002 1713643 1714351 1727012 1727678 1773544 1826726 1842866 1860661 1913291 2143780 
15.0 1.922 4.934 0.704 1.756 8.624 2.896 11.19 5.395 9.85 2.062 1.46 3.773 1.818 5.218 0.773 18.448 16.962 4.456 8.436 13.885 2.091 9.177 8.08 1.682 0.655 0.987 14.95 0.922 1.219 6.139 6.181 19.927 0.461 1.943 6.825 0.699 0.639 1.028 22.957 4.901 0.504 2.118 0.519 0.999 6.767 1.843 22.941 2.045 2.599 1.068 3.166 0.089 14.231 0.963 7.177 3.902 2.393 2.661 10.51 1.901 3.114 15.319 2.836 2.751 3.3 3.446 2.698 1.061 19.07 1.534 6.545 2.96 1.039 1.043 1.285 0.746 1.866 5.712 15.783 0.866 6.002 0.519 13.638 3.068 0.028 0.706 3.958 4.045 1.379 1.132 0.949 7.269 2.527 1.134 0.492 17.213 1.787 8.7 11.371 1.353 15.044 0.724 2.117 1.904 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_850_0.prm:46
 Score: 102.53399999999999, AlignedPeaks: 491209 606333 707374 995466 1194547 1357609 1470694 1711820 
0 259136 277159 372226 390230 466676 491209 535289 606333 707374 721319 734360 798838 821414 882421 882918 930454 938967 939459 994481 995466 1002995 1003482 1022462 1026523 1051022 1059535 1060027 1066537 1123497 1153540 1194547 1325628 1339600 1357609 1452671 1470694 1496743 1517893 1567977 1574915 1711820 
15.0 14.581 5.547 18.036 2.859 1.427 2.282 13.342 9.712 7.894 3.545 6.867 2.08 4.595 3.365 1.981 4.988 1.798 3.858 3.252 7.129 1.495 1.36 4.661 1.386 4.573 1.735 2.969 1.969 8.11 2.472 12.242 2.85 0.587 20.159 0.223 13.116 3.68 2.017 0.608 3.154 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_800_0.prm:381
 Score: 88.198, AlignedPeaks: 493124 594259 882280 1357508 1598531 
0 162850 163529 207852 257687 259036 260824 277058 277524 278523 295319 309242 314277 318894 393746 417732 420837 422069 422699 430944 440157 465024 491072 493124 507007 511168 578279 594259 595388 606454 636911 641497 672834 700429 708274 713071 734211 743924 764365 780681 794884 796382 817489 820159 821657 826107 881352 882280 888700 890099 898906 903471 908281 937823 946612 955466 979630 992111 1010038 1022296 1027811 1038262 1057095 1058882 1062656 1084388 1100225 1118224 1123409 1125442 1151517 1174141 1174893 1176385 1182436 1185974 1187368 1193843 1194499 1198809 1222796 1224193 1225384 1246105 1297647 1338018 1339017 1339484 1355718 1357508 1368289 1408689 1598531 
15.0 9.099 10.332 1.005 1.338 25.284 5.559 21.654 21.675 1.699 2.526 3.231 1.478 3.821 3.381 1.279 0.036 18.957 3.433 2.811 1.799 2.581 8.344 12.742 0.673 1.933 1.29 9.871 2.828 14.238 0.341 1.27 1.753 1.645 8.944 0.368 8.184 1.16 2.352 0.472 0.93 0.137 4.332 2.13 1.648 3.215 4.178 7.068 1.69 9.608 4.446 0.949 3.483 3.033 4.029 2.566 0.744 1.178 8.796 6.875 2.48 2.012 1.527 0.37 0.966 1.396 0.802 0.15 8.796 6.072 1.352 1.23 0.638 1.184 1.305 3.726 0.72 0.233 11.613 0.507 2.268 0.568 0.098 0.575 1.161 0.09 17.187 22.662 0.846 28.517 1.855 2.157 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_700_0.prm:30
 Score: 86.267, AlignedPeaks: 875340 1038339 1151331 1392570 
0 131110 170823 172044 243102 258228 259233 277074 287033 303276 304703 371159 372235 389453 390084 407158 415217 422438 502319 534183 535230 589207 591332 605344 606168 606843 624348 714344 723043 770801 779221 779892 788255 791393 804398 821348 834780 835788 843630 866247 875340 891314 900319 908276 935507 962430 978387 988143 995306 996456 1003423 1006444 1020497 1021128 1038339 1075531 1123533 1151331 1221541 1238537 1279471 1392570 
15.0 15.968 0.707 6.053 7.162 8.071 29.865 4.586 12.953 0.353 0.173 1.736 21.267 6.057 0.763 0.547 8.476 0.5 3.755 0.717 14.432 9.132 0.626 0.877 14.951 3.857 1.147 2.55 3.372 7.793 3.609 3.439 1.661 1.535 10.486 12.209 2.958 1.401 1.958 0.581 10.509 4.283 2.074 5.679 0.45 1.125 0.699 1.751 10.399 0.961 1.714 3.864 1.327 2.396 15.036 0.016 5.063 30.722 2.38 5.032 10.297 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:55.991499999999995, InsertsAfter: 11
 * M[1] - Mass:70962.63636363634 Overlap:6/6 LogOddsScore:7.846065189950238, SumScore:65.7361337458986, InsertsAfter: 20
 * M[2] - Mass:186098.0 Overlap:6/6 LogOddsScore:11.98456774111193, SumScore:127.22250000000001, InsertsAfter: 18
 * M[3] - Mass:287354.4166666666 Overlap:6/6 LogOddsScore:10.77382531477838, SumScore:109.82450000000001, InsertsAfter: 17
 * M[4] - Mass:374559.4285714286 Overlap:4/6 LogOddsScore:7.067029139314061, SumScore:75.21950000000001, InsertsAfter: 15
 * M[5] - Mass:461933.3333333333 Overlap:2/6 LogOddsScore:0.43247283902160016, SumScore:6.149, InsertsAfter: 27
 * M[6] - Mass:575226.2857142857 Overlap:4/6 LogOddsScore:6.560753867153017, SumScore:57.911133745898596, InsertsAfter: 28
 * M[7] - Mass:703281.7272727273 Overlap:4/6 LogOddsScore:4.139269014485919, SumScore:36.155, InsertsAfter: 16
 * M[8] - Mass:774305.7272727273 Overlap:6/6 LogOddsScore:9.056807616283788, SumScore:73.74913374589859, InsertsAfter: 33
 * M[9] - Mass:937340.8181818181 Overlap:6/6 LogOddsScore:12.942172531364955, SumScore:128.8032674917972, InsertsAfter: 13
 * M[10] - Mass:1050380.8333333337 Overlap:6/6 LogOddsScore:13.195310167445477, SumScore:146.09599999999998, InsertsAfter: 20
 * M[11] - Mass:1178254.75 Overlap:2/6 LogOddsScore:1.643215265355149, SumScore:26.08, InsertsAfter: 3
 * M[12] - Mass:1291558.5 Overlap:6/6 LogOddsScore:12.689034895284433, SumScore:87.276, InsertsAfter: 22
ConsensusPRM: 0 70962 186098 287354 374559 461933 575226 703281 774305 937340 1050380 1178254 1291558 Consensus: 0 70962 186098 287354 374559 461933 575226 703281 774305 937340 1050380 1178254 1291558
De Novo: ADTS[200.667]QAYIQI, Merged: [316.128]IWNEQFKGKATFTADTSSNQAYIQI
-316128 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 1302708 1449776 1550823 1621860 1736886 1837933 1924965 2011997 2012728 2126039 2254076 2324906 2488125 2601156 2729049 2842353 
11.761 45.82 55.736000000000004 104.4885 141.2515 165.89 129.341 89.602 45.166999999999994 30.0 37.5 43.331566872949296 37.7595 33.33356687294929 52.647999999999996 51.3226337458986 96.52450000000002 88.488 60.4386337458986 30.0 -7.198465016405639 44.26926749179719 29.481267491797183 51.95713374589859 86.13526749179718 98.61249999999998 12.732534983594359 57.956999999999994 
(RIGHT)Round: 2 for seed: [316.128]IWNEQFKGKATFTADTSSNQAYIQI
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_850_0.prm:57
 Score: 172.466, AlignedPeaks: 606272 707247 995357 1123363 1194478 1357503 1470485 1711613 
0 172052 231767 241231 248112 248534 258016 259149 276113 277083 295001 319198 337010 361161 371163 372130 389186 390198 407392 420170 422041 431137 448363 475042 491101 535131 535799 553226 578100 605567 606272 622305 624154 682424 690267 707247 717486 725232 734235 740650 743784 750267 781514 795219 821282 839434 853301 855789 873835 876323 882146 882880 891601 908379 930454 939162 948110 985877 994314 995357 1003094 1022366 1039356 1047199 1050946 1059704 1068650 1123363 1124057 1132298 1141349 1151524 1153354 1184857 1193825 1194478 1229450 1238564 1254581 1256564 1279382 1281260 1298486 1309445 1322232 1325559 1339426 1340438 1357503 1410426 1427959 1452541 1453494 1470485 1471608 1481089 1481511 1497856 1557572 1711613 
15.0 0.519 1.277 12.002 2.424 2.423 11.121 30.209 20.737 15.039 2.804 10.004 1.766 0.101 1.61 33.543 10.959 14.825 1.491 6.687 0.536 0.233 0.159 0.334 11.868 20.943 1.701 2.718 0.534 1.154 20.283 1.117 0.866 0.431 0.579 13.772 0.72 0.235 12.973 1.525 3.419 1.933 0.015 2.961 12.872 0.213 0.023 0.543 0.519 0.318 2.784 3.378 2.072 11.272 5.953 5.045 1.26 8.825 6.999 13.481 4.947 10.473 0.942 0.61 5.248 3.882 0.843 14.393 1.203 1.681 0.319 2.296 1.168 0.069 0.272 13.656 0.86 7.562 1.658 2.19 0.278 0.544 0.592 4.317 0.439 5.11 1.785 4.746 34.822 8.355 0.549 8.084 8.988 32.059 5.442 3.193 3.736 3.52 1.82 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:77
 Score: 127.478, AlignedPeaks: 434177 535193 622096 951424 1022367 1185357 1298438 1426562 1539704 
0 248500 250724 298429 301129 318924 326165 335089 351201 352507 363185 370277 388246 396928 405975 421240 434177 434778 439252 447439 448161 452268 464788 466242 482865 501002 528186 535193 552720 561050 561910 562351 622096 639283 640063 649325 666351 717317 732863 735233 735987 737481 752055 763919 793810 850428 861206 863337 870537 879522 881435 951424 964466 976398 994482 1022367 1098235 1098962 1107444 1139400 1154050 1163114 1185357 1197324 1198058 1206323 1210978 1257432 1282269 1298438 1304632 1311343 1313777 1375773 1409736 1414959 1419592 1424309 1425803 1426562 1462391 1512422 1522508 1539704 1549641 1567629 1594386 1599476 1600048 1600740 1609071 1609769 1626598 1633604 1660788 1697002 1713643 1714351 1727012 1727678 1773544 1826726 1842866 1860661 1913291 2143780 
15.0 1.922 4.934 0.704 1.756 8.624 2.896 11.19 5.395 9.85 2.062 1.46 3.773 1.818 5.218 0.773 18.448 16.962 4.456 8.436 13.885 2.091 9.177 8.08 1.682 0.655 0.987 14.95 0.922 1.219 6.139 6.181 19.927 0.461 1.943 6.825 0.699 0.639 1.028 22.957 4.901 0.504 2.118 0.519 0.999 6.767 1.843 22.941 2.045 2.599 1.068 3.166 0.089 14.231 0.963 7.177 3.902 2.393 2.661 10.51 1.901 3.114 15.319 2.836 2.751 3.3 3.446 2.698 1.061 19.07 1.534 6.545 2.96 1.039 1.043 1.285 0.746 1.866 5.712 15.783 0.866 6.002 0.519 13.638 3.068 0.028 0.706 3.958 4.045 1.379 1.132 0.949 7.269 2.527 1.134 0.492 17.213 1.787 8.7 11.371 1.353 15.044 0.724 2.117 1.904 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_850_0.prm:46
 Score: 108.36200000000001, AlignedPeaks: 606333 707374 995466 1123497 1194547 1357609 1470694 1711820 
0 259136 277159 372226 390230 466676 491209 535289 606333 707374 721319 734360 798838 821414 882421 882918 930454 938967 939459 994481 995466 1002995 1003482 1022462 1026523 1051022 1059535 1060027 1066537 1123497 1153540 1194547 1325628 1339600 1357609 1452671 1470694 1496743 1517893 1567977 1574915 1711820 
15.0 14.581 5.547 18.036 2.859 1.427 2.282 13.342 9.712 7.894 3.545 6.867 2.08 4.595 3.365 1.981 4.988 1.798 3.858 3.252 7.129 1.495 1.36 4.661 1.386 4.573 1.735 2.969 1.969 8.11 2.472 12.242 2.85 0.587 20.159 0.223 13.116 3.68 2.017 0.608 3.154 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_700_0.prm:30
 Score: 107.05, AlignedPeaks: 804398 875340 1038339 1151331 1279471 1392570 
0 131110 170823 172044 243102 258228 259233 277074 287033 303276 304703 371159 372235 389453 390084 407158 415217 422438 502319 534183 535230 589207 591332 605344 606168 606843 624348 714344 723043 770801 779221 779892 788255 791393 804398 821348 834780 835788 843630 866247 875340 891314 900319 908276 935507 962430 978387 988143 995306 996456 1003423 1006444 1020497 1021128 1038339 1075531 1123533 1151331 1221541 1238537 1279471 1392570 
15.0 15.968 0.707 6.053 7.162 8.071 29.865 4.586 12.953 0.353 0.173 1.736 21.267 6.057 0.763 0.547 8.476 0.5 3.755 0.717 14.432 9.132 0.626 0.877 14.951 3.857 1.147 2.55 3.372 7.793 3.609 3.439 1.661 1.535 10.486 12.209 2.958 1.401 1.958 0.581 10.509 4.283 2.074 5.679 0.45 1.125 0.699 1.751 10.399 0.961 1.714 3.864 1.327 2.396 15.036 0.016 5.063 30.722 2.38 5.032 10.297 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1050_0.prm:89
 Score: 97.989, AlignedPeaks: 261062 389121 460336 623160 736274 864253 977376 
0 261062 278867 286454 296266 305624 313135 331239 332052 350122 361201 389121 396891 398252 415361 424468 433307 437607 442154 448151 451314 460336 464185 469390 497519 528210 543267 580273 598296 623160 630754 640338 681342 699347 717328 736274 752350 753018 770131 788387 845294 847123 849143 853351 864253 871692 882320 898429 909188 941264 975096 977376 984493 1048150 1069760 1071594 1074319 1076864 1085448 1089708 1095359 1109283 1140478 1151507 1158630 1219481 1253661 1264557 1268767 1270787 1290821 1364875 1365555 1381601 1399623 1409008 1425551 1436575 1476307 1486612 1494761 1501439 1512810 1537587 1538783 1541941 1547740 1555671 1567681 1574643 1589700 1620391 1638794 1657574 1684637 1785908 1804775 1811788 1812286 1821644 1831456 1839043 1856848 1955400 2099900 
15.0 4.673 5.599 2.832 1.412 5.121 2.172 5.221 10.832 2.144 3.234 7.059 1.942 1.096 0.824 6.637 12.919 1.051 0.535 1.595 13.745 13.565 8.057 5.061 2.293 0.705 0.263 7.884 3.674 17.945 1.33 1.561 3.671 6.244 1.868 19.728 11.931 8.773 2.466 0.987 1.742 0.837 1.648 4.906 15.73 12.592 1.546 0.659 3.068 3.068 3.356 19.289 5.166 0.451 2.012 1.173 3.155 3.939 4.344 2.03 2.095 2.212 10.112 6.023 0.595 1.435 11.023 19.212 1.624 0.844 0.972 7.575 18.699 3.147 5.372 1.31 2.17 11.464 0.445 1.99 4.821 0.423 3.11 14.731 0.84 1.362 1.591 1.107 1.32 0.609 0.515 1.668 1.296 2.528 18.164 11.637 3.29 3.952 4.079 2.307 2.405 7.457 5.255 4.427 15.0 

SpectrumHMM Model: * M[0] - Mass:-38.888888888888886 Overlap:6/6 LogOddsScore:11.98456774111193, SumScore:157.9205, InsertsAfter: 18
 * M[1] - Mass:101289.0 Overlap:6/6 LogOddsScore:10.77382531477838, SumScore:131.161, InsertsAfter: 18
 * M[2] - Mass:188362.2 Overlap:4/7 LogOddsScore:6.723098987629199, SumScore:83.32663374589859, InsertsAfter: 15
 * M[3] - Mass:275807.0 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:6.149, InsertsAfter: 27
 * M[4] - Mass:389127.85714285716 Overlap:5/7 LogOddsScore:7.4648505900335405, SumScore:69.5522674917972, InsertsAfter: 37
 * M[5] - Mass:517181.63636363635 Overlap:7/7 LogOddsScore:9.96090433916431, SumScore:72.69526749179718, InsertsAfter: 25
 * M[6] - Mass:588214.3636363636 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:109.1061337458986, InsertsAfter: 40
 * M[7] - Mass:751216.0909090908 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:189.41626749179716, InsertsAfter: 18
 * M[8] - Mass:864265.0909090909 Overlap:7/7 LogOddsScore:15.816424588820594, SumScore:213.30749999999998, InsertsAfter: 28
 * M[9] - Mass:992306.7142857143 Overlap:5/7 LogOddsScore:6.254108163699992, SumScore:54.542534983594365, InsertsAfter: 9
 * M[10] - Mass:1105439.5454545459 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:135.88400000000001, InsertsAfter: 32
 * M[11] - Mass:1392598.5 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:34.256, InsertsAfter: 41
ConsensusPRM: -38 101289 188362 275807 389127 517181 588214 751216 864265 992306 1105439 1392598 Consensus: -38 101289 188362 275807 389127 517181 588214 751216 864265 992306 1105439 1392598
De Novo: TS[200.765]QAYIQI[287.159], Merged: [316.128]IWNEQFKGKATFTADTSSNQAYIQI[287.159]
-316128 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 1302708 1449776 1550823 1621860 1736886 1837933 1924965 2011997 2012721 2126039 2254076 2324906 2488125 2601156 2729049 2842353 3129512 
11.761 45.82 55.736000000000004 104.4885 141.2515 165.89 129.341 89.602 45.166999999999994 30.0 37.5 43.331566872949296 37.7595 33.33356687294929 52.647999999999996 51.3226337458986 127.22250000000001 109.8245 66.87733436474647 30.0 -10.535331270507047 53.57390123769578 51.08826749179718 80.5316337458986 137.77576749179718 155.95999999999998 30.300668729492955 96.9205 34.256 
(RIGHT)Round: 3 for seed: [316.128]IWNEQFKGKATFTADTSSNQAYIQI[287.159]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:77
 Score: 124.074, AlignedPeaks: 535193 622096 951424 1022367 1185357 1298438 1426562 1539704 1826726 
0 248500 250724 298429 301129 318924 326165 335089 351201 352507 363185 370277 388246 396928 405975 421240 434177 434778 439252 447439 448161 452268 464788 466242 482865 501002 528186 535193 552720 561050 561910 562351 622096 639283 640063 649325 666351 717317 732863 735233 735987 737481 752055 763919 793810 850428 861206 863337 870537 879522 881435 951424 964466 976398 994482 1022367 1098235 1098962 1107444 1139400 1154050 1163114 1185357 1197324 1198058 1206323 1210978 1257432 1282269 1298438 1304632 1311343 1313777 1375773 1409736 1414959 1419592 1424309 1425803 1426562 1462391 1512422 1522508 1539704 1549641 1567629 1594386 1599476 1600048 1600740 1609071 1609769 1626598 1633604 1660788 1697002 1713643 1714351 1727012 1727678 1773544 1826726 1842866 1860661 1913291 2143780 
15.0 1.922 4.934 0.704 1.756 8.624 2.896 11.19 5.395 9.85 2.062 1.46 3.773 1.818 5.218 0.773 18.448 16.962 4.456 8.436 13.885 2.091 9.177 8.08 1.682 0.655 0.987 14.95 0.922 1.219 6.139 6.181 19.927 0.461 1.943 6.825 0.699 0.639 1.028 22.957 4.901 0.504 2.118 0.519 0.999 6.767 1.843 22.941 2.045 2.599 1.068 3.166 0.089 14.231 0.963 7.177 3.902 2.393 2.661 10.51 1.901 3.114 15.319 2.836 2.751 3.3 3.446 2.698 1.061 19.07 1.534 6.545 2.96 1.039 1.043 1.285 0.746 1.866 5.712 15.783 0.866 6.002 0.519 13.638 3.068 0.028 0.706 3.958 4.045 1.379 1.132 0.949 7.269 2.527 1.134 0.492 17.213 1.787 8.7 11.371 1.353 15.044 0.724 2.117 1.904 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1050_0.prm:89
 Score: 117.20100000000001, AlignedPeaks: 261062 389121 460336 623160 736274 864253 977376 1264557 
0 261062 278867 286454 296266 305624 313135 331239 332052 350122 361201 389121 396891 398252 415361 424468 433307 437607 442154 448151 451314 460336 464185 469390 497519 528210 543267 580273 598296 623160 630754 640338 681342 699347 717328 736274 752350 753018 770131 788387 845294 847123 849143 853351 864253 871692 882320 898429 909188 941264 975096 977376 984493 1048150 1069760 1071594 1074319 1076864 1085448 1089708 1095359 1109283 1140478 1151507 1158630 1219481 1253661 1264557 1268767 1270787 1290821 1364875 1365555 1381601 1399623 1409008 1425551 1436575 1476307 1486612 1494761 1501439 1512810 1537587 1538783 1541941 1547740 1555671 1567681 1574643 1589700 1620391 1638794 1657574 1684637 1785908 1804775 1811788 1812286 1821644 1831456 1839043 1856848 1955400 2099900 
15.0 4.673 5.599 2.832 1.412 5.121 2.172 5.221 10.832 2.144 3.234 7.059 1.942 1.096 0.824 6.637 12.919 1.051 0.535 1.595 13.745 13.565 8.057 5.061 2.293 0.705 0.263 7.884 3.674 17.945 1.33 1.561 3.671 6.244 1.868 19.728 11.931 8.773 2.466 0.987 1.742 0.837 1.648 4.906 15.73 12.592 1.546 0.659 3.068 3.068 3.356 19.289 5.166 0.451 2.012 1.173 3.155 3.939 4.344 2.03 2.095 2.212 10.112 6.023 0.595 1.435 11.023 19.212 1.624 0.844 0.972 7.575 18.699 3.147 5.372 1.31 2.17 11.464 0.445 1.99 4.821 0.423 3.11 14.731 0.84 1.362 1.591 1.107 1.32 0.609 0.515 1.668 1.296 2.528 18.164 11.637 3.29 3.952 4.079 2.307 2.405 7.457 5.255 4.427 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1000_0.prm:163
 Score: 104.102, AlignedPeaks: 703487 774210 937392 1050513 1178479 1291588 1578608 
0 215048 234001 240369 262297 286291 291259 299249 309064 313421 314367 318248 331198 332432 348361 349327 352045 354022 366973 370058 388139 401254 419536 439035 449399 450315 457250 468429 475088 481070 488265 498871 517226 562474 563391 585482 602415 604163 649531 650442 668438 685180 703487 736380 737341 748702 755450 774210 774680 798341 804172 830968 849509 850414 864346 868604 904700 907505 921415 925737 936632 937392 977572 978388 996480 1032507 1049706 1050513 1081007 1089576 1090285 1091492 1098880 1107599 1154478 1164668 1178479 1189302 1198046 1224842 1254334 1254804 1272756 1289698 1291588 1325415 1330449 1343834 1365889 1378502 1412171 1424851 1426556 1440853 1442712 1443532 1447577 1460816 1465551 1466540 1490964 1511788 1530143 1540645 1547944 1549620 1553926 1560585 1571764 1578608 1627709 1679658 1697829 1714634 1715593 1766717 1795013 1796340 1853393 2011004 
15.0 1.769 1.807 1.786 3.164 0.709 0.909 0.116 0.812 2.916 14.408 2.406 5.78 5.167 3.297 19.295 0.475 0.142 8.43 1.322 1.029 6.899 2.6 0.203 5.594 15.706 0.68 2.692 1.336 2.148 8.936 1.165 0.854 0.982 9.274 0.703 9.579 0.635 1.36 12.802 0.305 0.231 11.538 2.485 14.361 3.057 1.417 15.686 17.6 0.222 0.219 0.214 2.479 16.909 0.686 2.338 2.983 3.326 0.721 1.78 2.146 13.625 2.812 16.784 7.364 8.53 1.327 15.999 3.366 2.64 3.654 9.943 1.602 2.651 2.681 2.154 15.441 1.378 3.289 2.143 13.77 11.174 2.854 1.989 12.45 7.387 1.847 2.108 0.325 9.45 0.779 3.461 5.548 2.267 2.084 0.792 0.96 0.508 8.647 0.847 0.784 2.227 2.406 10.629 2.843 1.137 2.038 1.416 0.541 19.363 8.737 21.586 7.447 11.77 0.188 10.717 1.35 1.867 1.225 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:165
 Score: 103.55099999999999, AlignedPeaks: 703334 774336 937344 1050404 1178424 1291495 1578595 
0 207940 231863 234022 251297 251629 273211 283150 296155 299159 314201 328254 335177 352309 352863 353252 370147 388127 401303 404121 448212 457072 475143 488287 493035 535164 535843 553322 602320 611113 620187 622245 640363 703334 735325 753297 774336 792354 810426 831489 863347 881453 937344 974679 976418 983666 1030257 1038682 1039314 1048242 1050404 1073848 1082291 1082959 1139412 1157455 1174469 1178424 1189549 1210391 1228512 1272471 1275527 1291495 1302667 1311376 1312235 1325492 1327524 1360458 1377937 1378604 1385565 1396603 1414533 1420745 1425478 1438635 1447536 1456708 1465563 1512459 1525653 1543672 1561471 1578595 1599589 1614621 1662151 1679758 1680574 1681917 1705840 1895769 
15.0 2.057 0.936 8.123 3.187 4.14 2.009 0.39 1.13 0.19 9.513 0.754 18.883 2.413 10.639 6.228 5.391 2.715 10.62 1.595 10.704 0.241 5.266 6.733 1.726 15.744 0.946 0.688 6.98 0.151 0.502 21.1 3.034 8.895 16.024 0.451 17.103 0.408 1.567 0.222 16.802 0.957 8.521 4.471 11.017 1.205 2.37 1.272 3.021 2.07 17.428 4.08 2.52 2.406 15.9 2.738 1.696 15.707 1.799 7.505 1.808 1.298 2.593 15.014 1.262 9.997 0.826 2.978 0.649 1.143 0.925 10.4 0.171 0.27 0.493 1.019 7.864 7.607 1.279 2.864 9.84 2.563 1.873 7.228 3.027 20.883 6.929 0.402 1.001 12.498 6.127 0.871 1.682 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1050_0.prm:23
 Score: 95.068, AlignedPeaks: 261053 389034 460126 623049 736227 864206 977263 1264428 
0 261053 277992 283934 288276 313098 332184 337597 348201 349089 356128 371319 389034 404352 425260 431969 432695 447621 449876 451447 454929 460126 466882 469496 476806 479286 485846 508111 521263 570140 580432 582109 598081 612137 616558 622050 623049 639857 651219 681222 698331 708881 710870 716552 719335 736227 752391 834534 846269 847639 853351 864206 871436 872775 906567 954392 960492 968551 974670 977263 993641 996572 1010639 1016972 1037210 1071060 1078295 1080604 1082667 1124090 1126174 1140622 1142408 1157322 1193003 1245039 1264428 1270175 1282234 1287420 1294708 1339973 1345360 1365441 1381570 1383291 1389507 1398479 1401262 1408933 1416250 1419484 1436638 1466595 1483314 1494668 1495764 1512748 1519734 1535705 1537380 1547674 1562605 1597994 1609400 1616418 1631968 1638528 1641014 1657729 1662885 1684449 1697598 1746495 1761686 1768725 1785620 1804716 1829538 1833880 1839822 1856761 1895275 1955661 2099804 
15.0 4.726 2.828 2.915 1.494 3.022 7.821 2.354 0.993 5.732 2.344 6.138 5.062 2.701 1.893 6.029 2.564 2.664 1.992 6.516 1.985 12.975 5.791 6.029 4.58 4.318 2.379 4.672 0.729 0.19 7.749 0.548 5.418 2.886 0.699 10.805 12.199 1.318 2.871 7.482 1.736 2.323 3.104 2.068 1.753 14.009 12.889 3.004 1.683 1.706 10.938 6.868 7.594 0.811 3.169 6.267 0.331 2.969 4.028 18.747 8.189 3.3 1.606 3.502 0.112 2.087 6.121 2.596 2.629 11.248 2.926 11.829 3.201 4.42 1.904 1.095 20.482 2.081 2.41 1.628 0.566 1.411 1.746 12.063 2.981 0.8 1.877 1.54 0.147 0.025 2.563 0.907 14.354 0.164 0.841 5.427 4.038 0.786 0.684 1.463 13.451 2.791 2.238 1.945 5.444 1.064 0.823 1.737 3.831 14.002 2.956 5.81 0.476 0.551 0.384 0.614 11.721 1.831 2.186 3.048 2.986 5.383 2.29 6.678 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:124.7745, InsertsAfter: 29
 * M[1] - Mass:86924.49999999999 Overlap:3/7 LogOddsScore:5.475072113063814, SumScore:86.80433436474647, InsertsAfter: 16
 * M[2] - Mass:174064.0 Overlap:2/7 LogOddsScore:2.5100275400038363, SumScore:30.0, InsertsAfter: 22
 * M[3] - Mass:288106.0 Overlap:4/7 LogOddsScore:5.51235656129565, SumScore:62.97290123769578, InsertsAfter: 37
 * M[4] - Mass:416164.9 Overlap:7/7 LogOddsScore:8.750161912830762, SumScore:86.80826749179717, InsertsAfter: 27
 * M[5] - Mass:487244.0 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:148.9516337458986, InsertsAfter: 44
 * M[6] - Mass:650144.35 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:205.38476749179716, InsertsAfter: 31
 * M[7] - Mass:763245.65 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:242.19399999999996, InsertsAfter: 36
 * M[8] - Mass:891260.1500000001 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:99.82966872949297, InsertsAfter: 28
 * M[9] - Mass:1004379.7500000002 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:176.05850000000004, InsertsAfter: 26
 * M[10] - Mass:1091317.3636363635 Overlap:3/7 LogOddsScore:1.3365695619021236, SumScore:27.119, InsertsAfter: 36
 * M[11] - Mass:1178408.7647058824 Overlap:4/7 LogOddsScore:3.7953388628010574, SumScore:41.723, InsertsAfter: 24
 * M[12] - Mass:1291473.9500000002 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:129.24, InsertsAfter: 17
 * M[13] - Mass:1392487.7692307688 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:64.84599999999999, InsertsAfter: 35
 * M[14] - Mass:1564532.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:28.182000000000002, InsertsAfter: 9
 * M[15] - Mass:1608582.5 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 36
 * M[16] - Mass:2126900.5 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 0
ConsensusPRM: 0 86924 174064 288106 416164 487244 650144 763245 891260 1004379 1091317 1178408 1291473 1392487 1564532 1608582 2126900 Consensus: 0 86924 174064 288106 416164 487244 650144 763245 891260 1004379 1091317 1178408 1291473 1392487 1564532 1608582 2126900
De Novo: SSNQAYIQISSIT[216.095], Merged: [316.128]IWNEQFKGKATFTADTSSNQAYIQISSIT[216.095]
-316128 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 1302708 1449776 1550823 1621860 1736886 1837933 1924965 2011997 2126039 2254076 2324906 2488125 2601156 2729049 2842353 2929356 3016447 3129512 3230526 3402571 3446621 3964939 
11.761 45.82 55.736000000000004 104.4885 141.2515 165.89 129.341 89.602 45.166999999999994 30.0 37.5 43.331566872949296 37.7595 33.33356687294929 52.647999999999996 51.3226337458986 127.22250000000001 117.2995 70.16710185654365 21.657834364746478 53.268101856543666 68.94826749179717 114.7416337458986 171.58026749179717 199.07699999999997 65.06516872949297 136.48950000000002 13.77153498359436 31.71240123769577 81.748 61.50913374589858 18.171401237695772 19.98940123769577 30.0 
(RIGHT)Round: 4 for seed: [316.128]IWNEQFKGKATFTADTSSNQAYIQISSIT[216.095]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:165
 Score: 166.289, AlignedPeaks: 703334 774336 937344 1050404 1178424 1291495 1378604 1465563 1578595 1679758 1895769 
0 207940 231863 234022 251297 251629 273211 283150 296155 299159 314201 328254 335177 352309 352863 353252 370147 388127 401303 404121 448212 457072 475143 488287 493035 535164 535843 553322 602320 611113 620187 622245 640363 703334 735325 753297 774336 792354 810426 831489 863347 881453 937344 974679 976418 983666 1030257 1038682 1039314 1048242 1050404 1073848 1082291 1082959 1139412 1157455 1174469 1178424 1189549 1210391 1228512 1272471 1275527 1291495 1302667 1311376 1312235 1325492 1327524 1360458 1377937 1378604 1385565 1396603 1414533 1420745 1425478 1438635 1447536 1456708 1465563 1512459 1525653 1543672 1561471 1578595 1599589 1614621 1662151 1679758 1680574 1681917 1705840 1895769 
15.0 2.057 0.936 8.123 3.187 4.14 2.009 0.39 1.13 0.19 9.513 0.754 18.883 2.413 10.639 6.228 5.391 2.715 10.62 1.595 10.704 0.241 5.266 6.733 1.726 15.744 0.946 0.688 6.98 0.151 0.502 21.1 3.034 8.895 16.024 0.451 17.103 0.408 1.567 0.222 16.802 0.957 8.521 4.471 11.017 1.205 2.37 1.272 3.021 2.07 17.428 4.08 2.52 2.406 15.9 2.738 1.696 15.707 1.799 7.505 1.808 1.298 2.593 15.014 1.262 9.997 0.826 2.978 0.649 1.143 0.925 10.4 0.171 0.27 0.493 1.019 7.864 7.607 1.279 2.864 9.84 2.563 1.873 7.228 3.027 20.883 6.929 0.402 1.001 12.498 6.127 0.871 1.682 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:421
 Score: 151.392, AlignedPeaks: 517279 588310 751297 992416 1105465 1192469 1279529 1392559 1493619 1709718 
0 128580 215232 216069 234110 250234 252096 269022 299217 311235 334027 335174 352226 353154 362204 370195 380286 416297 439097 447203 448204 465066 466163 475265 510373 517279 534223 535234 587392 588310 606350 621147 622234 733169 734315 735285 735974 750376 751297 752015 753363 769444 771344 845278 846463 880347 881576 882025 882451 891053 899382 937435 946247 955201 976411 980814 989720 992416 998735 1011529 1040441 1046384 1049317 1098578 1103547 1105465 1115489 1121379 1133418 1139387 1157451 1192469 1210392 1216537 1217355 1228506 1234598 1246446 1252464 1261566 1262663 1279529 1280526 1288632 1311430 1312383 1339588 1365507 1392559 1393702 1416557 1425464 1428512 1454559 1493619 1494685 1495253 1511660 1513856 1582084 1709718 
15.0 1.029 3.517 0.422 13.899 0.039 2.996 2.414 0.759 2.736 6.043 23.906 5.741 9.096 6.698 4.857 6.444 6.56 0.376 0.153 10.881 0.203 1.144 1.028 0.115 7.742 0.634 12.31 0.919 16.697 0.546 6.028 19.229 0.292 4.251 12.459 0.322 3.599 14.32 3.018 2.896 1.115 0.815 0.006 0.39 1.917 7.346 1.822 2.609 2.226 0.503 0.569 4.025 2.825 14.93 2.218 3.158 11.075 0.347 1.773 2.957 2.595 2.687 0.769 0.411 13.986 2.541 0.067 1.189 16.374 0.238 6.808 10.616 1.434 1.126 1.893 1.074 1.077 1.197 0.668 3.943 6.963 0.424 1.266 4.137 1.1 3.29 9.466 27.668 0.286 3.162 3.476 4.333 0.791 16.133 10.125 2.288 8.996 1.537 2.82 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_800_0.prm:677
 Score: 149.625, AlignedPeaks: 1251597 1322688 1485730 1598741 1726861 1839828 1926914 2013705 2126924 2227904 2444016 
0 147452 234117 250820 252186 273069 274313 283185 299261 317254 333828 335098 352338 388117 447382 448298 465506 475082 501096 509444 517366 534674 535112 575253 575931 616751 617427 622198 626047 652548 661533 703288 734110 735165 736885 743036 749694 759915 765851 790584 794291 796451 799572 800434 808958 855165 856293 862553 863284 878542 895513 911656 921098 941624 949537 955166 963676 968093 971158 976292 983435 991731 998262 1006847 1007628 1022879 1036628 1053311 1054844 1063461 1064099 1086723 1105603 1113950 1114580 1131635 1138321 1139338 1148752 1150591 1157287 1170532 1184386 1193525 1210429 1251597 1268501 1277640 1291494 1304065 1304739 1311435 1313274 1322688 1323705 1330376 1348081 1356423 1375303 1397927 1398565 1407182 1425397 1439147 1454398 1455179 1463764 1478591 1485730 1490868 1493933 1498350 1506860 1512489 1520402 1540928 1541902 1550370 1566513 1583484 1598741 1599473 1606861 1615745 1653068 1656183 1658513 1661592 1662454 1665575 1667735 1696175 1702111 1712332 1718990 1725141 1726861 1727916 1758738 1796493 1799667 1800493 1809478 1835979 1839828 1842196 1844599 1845275 1886095 1886773 1926914 1927352 1944659 1960930 1986944 1996523 2013705 2014644 2040732 2073909 2109688 2126924 2144772 2150673 2162765 2178841 2187713 2188957 2212904 2227904 2229160 2314574 2315922 2444016 
15.0 2.287 12.832 1.649 2.283 0.601 1.26 3.858 0.915 2.971 3.574 18.73 0.797 1.817 8.418 12.651 14.232 5.486 2.085 3.71 0.635 12.461 16.625 1.997 1.78 2.875 3.293 11.004 1.577 4.261 3.812 1.985 4.523 8.13 1.594 2.92 0.976 3.463 0.448 0.418 4.814 2.115 0.716 1.769 0.256 5.236 1.605 5.95 10.932 1.924 3.772 2.007 2.215 3.764 4.595 0.348 1.262 1.633 0.5 15.924 1.685 3.748 0.689 1.219 1.027 3.075 4.648 2.025 5.577 3.32 0.025 5.29 1.969 4.573 1.494 11.21 9.328 9.919 2.662 5.146 9.043 2.647 1.491 2.248 6.187 7.624 0.713 1.886 2.639 0.367 5.613 6.169 2.588 10.527 6.523 10.142 11.745 1.079 2.552 2.025 3.291 5.046 6.678 1.514 0.169 1.498 1.777 0.287 15.945 2.079 0.534 3.388 2.482 3.214 0.874 1.536 2.094 3.516 6.559 2.307 12.252 2.682 4.61 1.817 1.235 0.432 3.984 0.529 7.206 1.952 2.221 1.676 4.577 0.847 5.37 3.879 7.918 4.477 3.474 2.218 3.431 6.016 3.277 3.008 12.213 1.438 2.739 3.124 3.77 3.583 13.736 12.99 1.291 0.25 0.894 8.56 12.506 5.502 0.139 1.808 0.639 16.722 3.502 0.518 1.715 0.648 0.024 1.816 1.292 10.182 5.588 4.253 4.078 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1000_0.prm:163
 Score: 143.78500000000003, AlignedPeaks: 703487 774210 937392 1050513 1178479 1291588 1378502 1465551 1578608 1679658 
0 215048 234001 240369 262297 286291 291259 299249 309064 313421 314367 318248 331198 332432 348361 349327 352045 354022 366973 370058 388139 401254 419536 439035 449399 450315 457250 468429 475088 481070 488265 498871 517226 562474 563391 585482 602415 604163 649531 650442 668438 685180 703487 736380 737341 748702 755450 774210 774680 798341 804172 830968 849509 850414 864346 868604 904700 907505 921415 925737 936632 937392 977572 978388 996480 1032507 1049706 1050513 1081007 1089576 1090285 1091492 1098880 1107599 1154478 1164668 1178479 1189302 1198046 1224842 1254334 1254804 1272756 1289698 1291588 1325415 1330449 1343834 1365889 1378502 1412171 1424851 1426556 1440853 1442712 1443532 1447577 1460816 1465551 1466540 1490964 1511788 1530143 1540645 1547944 1549620 1553926 1560585 1571764 1578608 1627709 1679658 1697829 1714634 1715593 1766717 1795013 1796340 1853393 2011004 
15.0 1.769 1.807 1.786 3.164 0.709 0.909 0.116 0.812 2.916 14.408 2.406 5.78 5.167 3.297 19.295 0.475 0.142 8.43 1.322 1.029 6.899 2.6 0.203 5.594 15.706 0.68 2.692 1.336 2.148 8.936 1.165 0.854 0.982 9.274 0.703 9.579 0.635 1.36 12.802 0.305 0.231 11.538 2.485 14.361 3.057 1.417 15.686 17.6 0.222 0.219 0.214 2.479 16.909 0.686 2.338 2.983 3.326 0.721 1.78 2.146 13.625 2.812 16.784 7.364 8.53 1.327 15.999 3.366 2.64 3.654 9.943 1.602 2.651 2.681 2.154 15.441 1.378 3.289 2.143 13.77 11.174 2.854 1.989 12.45 7.387 1.847 2.108 0.325 9.45 0.779 3.461 5.548 2.267 2.084 0.792 0.96 0.508 8.647 0.847 0.784 2.227 2.406 10.629 2.843 1.137 2.038 1.416 0.541 19.363 8.737 21.586 7.447 11.77 0.188 10.717 1.35 1.867 1.225 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:77
 Score: 143.67900000000003, AlignedPeaks: 951424 1022367 1185357 1298438 1426562 1539704 1626598 1713643 1826726 2143780 
0 248500 250724 298429 301129 318924 326165 335089 351201 352507 363185 370277 388246 396928 405975 421240 434177 434778 439252 447439 448161 452268 464788 466242 482865 501002 528186 535193 552720 561050 561910 562351 622096 639283 640063 649325 666351 717317 732863 735233 735987 737481 752055 763919 793810 850428 861206 863337 870537 879522 881435 951424 964466 976398 994482 1022367 1098235 1098962 1107444 1139400 1154050 1163114 1185357 1197324 1198058 1206323 1210978 1257432 1282269 1298438 1304632 1311343 1313777 1375773 1409736 1414959 1419592 1424309 1425803 1426562 1462391 1512422 1522508 1539704 1549641 1567629 1594386 1599476 1600048 1600740 1609071 1609769 1626598 1633604 1660788 1697002 1713643 1714351 1727012 1727678 1773544 1826726 1842866 1860661 1913291 2143780 
15.0 1.922 4.934 0.704 1.756 8.624 2.896 11.19 5.395 9.85 2.062 1.46 3.773 1.818 5.218 0.773 18.448 16.962 4.456 8.436 13.885 2.091 9.177 8.08 1.682 0.655 0.987 14.95 0.922 1.219 6.139 6.181 19.927 0.461 1.943 6.825 0.699 0.639 1.028 22.957 4.901 0.504 2.118 0.519 0.999 6.767 1.843 22.941 2.045 2.599 1.068 3.166 0.089 14.231 0.963 7.177 3.902 2.393 2.661 10.51 1.901 3.114 15.319 2.836 2.751 3.3 3.446 2.698 1.061 19.07 1.534 6.545 2.96 1.039 1.043 1.285 0.746 1.866 5.712 15.783 0.866 6.002 0.519 13.638 3.068 0.028 0.706 3.958 4.045 1.379 1.132 0.949 7.269 2.527 1.134 0.492 17.213 1.787 8.7 11.371 1.353 15.044 0.724 2.117 1.904 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:107.91326749179716, InsertsAfter: 20
 * M[1] - Mass:71015.375 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:183.84563374589857, InsertsAfter: 45
 * M[2] - Mass:234009.5 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:239.31026749179713, InsertsAfter: 35
 * M[3] - Mass:347067.3333333334 Overlap:6/7 LogOddsScore:11.640637589427067, SumScore:263.82599999999996, InsertsAfter: 50
 * M[4] - Mass:475102.625 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:130.98916872949297, InsertsAfter: 29
 * M[5] - Mass:588197.8749999999 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:203.7905, InsertsAfter: 29
 * M[6] - Mass:675213.25 Overlap:7/7 LogOddsScore:7.539419486497213, SumScore:61.43453498359437, InsertsAfter: 33
 * M[7] - Mass:762215.0 Overlap:7/7 LogOddsScore:9.96090433916431, SumScore:86.88140123769577, InsertsAfter: 28
 * M[8] - Mass:875283.5 Overlap:7/7 LogOddsScore:15.563286952740071, SumScore:181.42800000000003, InsertsAfter: 19
 * M[9] - Mass:976350.8571428572 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:121.90813374589858, InsertsAfter: 0
 * M[10] - Mass:977371.0 Overlap:3/7 LogOddsScore:1.3365695619021236, SumScore:21.84, InsertsAfter: 15
 * M[11] - Mass:1192438.2857142857 Overlap:6/7 LogOddsScore:9.923619890932475, SumScore:79.98940123769577, InsertsAfter: 1
ConsensusPRM: 0 71015 234009 347067 475102 588197 675213 762215 875283 976350 977371 1192438 Consensus: 0 71015 234009 347067 475102 588197 675213 762215 875283 976350 977371 1192438
De Novo: AYIQISSIT[216.088], Merged: [316.128]IWNEQFKGKATFTADTSSNQAYIQISSIT[216.095]
-316128 0 113086 299109 413218 542318 670343 817334 945684 1002530 1130624 1201424 1302708 1449776 1550823 1621860 1736886 1837933 1924965 2011997 2126039 2254076 2324906 2488125 2601156 2729049 2842353 2929356 3016447 3129512 3230526 3231554 3446621 
11.761 45.82 55.736000000000004 104.4885 141.2515 165.89 129.341 89.602 45.166999999999994 30.0 37.5 43.331566872949296 37.7595 33.33356687294929 52.647999999999996 51.3226337458986 127.22250000000001 117.2995 70.16710185654365 21.657834364746478 53.268101856543666 88.43076749179716 149.29363374589857 205.44526749179715 229.78306687294923 98.02716872949297 170.14000000000001 37.60303498359436 59.29690123769577 131.58800000000002 90.04020061884788 8.49253498359436 48.32096811064507 

(LEFT)Round: 0 for seed: AKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPNLEGGPSVFIFPPNIKDVLMISLTPKVTC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1250_0.prm:63
 Score: 114.73300000000002, AlignedPeaks: 445260 573224 674298 775266 872372 969537 1056438 1155502 1318528 1415578 
0 198835 199521 200091 225963 262031 286841 356450 379187 409205 424087 427105 433303 438259 445260 451304 474035 486190 488202 520347 556315 557354 569229 573224 575296 587224 612269 622865 623291 670291 674298 731263 775266 775779 783209 793272 824451 832305 840207 872372 937268 955349 969537 973305 1008290 1008842 1026260 1031454 1045835 1056438 1121365 1125051 1137438 1155502 1218402 1236399 1254455 1286196 1318528 1320782 1329790 1367890 1368233 1368518 1381432 1392831 1399537 1411893 1415578 1418544 1480496 1491109 1528663 1563639 1567407 1581651 1599703 1635683 1663587 1664577 1668651 1696773 1704639 1712493 1725687 1743672 1753730 1761165 1761709 1779602 1797605 1826614 1862684 1913813 1914079 1924675 1961648 2109839 2127739 2157757 2180494 
15.0 1.923 1.469 2.1 6.581 2.069 1.768 2.744 3.625 3.745 5.762 5.552 4.523 3.31 12.073 1.437 5.58 5.203 3.616 8.201 4.594 5.401 5.126 9.452 1.621 0.028 1.056 3.574 8.09 1.026 12.995 1.903 27.471 8.755 5.247 3.009 2.35 1.852 3.641 6.79 19.183 9.154 0.26 0.001 17.795 1.734 0.039 1.031 0.535 8.286 2.064 0.212 2.838 18.29 16.193 2.733 1.077 2.899 17.885 3.196 2.461 1.651 0.437 2.798 16.057 1.992 5.53 0.543 1.231 1.624 6.484 0.825 18.934 1.475 0.698 3.544 20.287 0.04 2.329 3.292 0.292 7.053 1.268 0.567 1.447 0.378 6.842 21.447 19.363 2.372 1.865 2.181 1.681 3.432 1.367 2.446 1.623 2.687 0.947 1.17 1.922 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:227
 Score: 102.41499999999999, AlignedPeaks: 445097 573272 674289 775344 872691 969524 1155268 1318401 1415568 
0 136651 173825 217690 235683 281050 281335 294289 295481 304986 318037 319937 321091 330162 380226 425751 427020 445097 446479 449097 460128 462207 488238 498079 546985 550449 557703 573272 575216 594039 641388 645354 650203 659340 674289 709249 753276 755285 764339 775344 781916 790891 799913 824342 827498 860655 866675 872691 900320 957027 969524 972009 978832 980788 981494 983149 983605 985815 986227 1000331 1001035 1018283 1055614 1069601 1071387 1074130 1089555 1137303 1138343 1146227 1149186 1154011 1155268 1160011 1172472 1173389 1206009 1207864 1208438 1209388 1215931 1222377 1224346 1250565 1259562 1268742 1274304 1281494 1292332 1300081 1309068 1310641 1317274 1318401 1319474 1321245 1325024 1336405 1400408 1415568 1417340 1418450 1419539 1426172 1427139 1427745 1436732 1444481 1455319 1462509 1468160 1477251 1486248 1512467 1520882 1527425 1528375 1528940 1530804 1534771 1564341 1576802 1581596 1582802 1587627 1590586 1590926 1598471 1599511 1617446 1643620 1647258 1662683 1665426 1680477 1718530 1736482 1750586 1750998 1753208 1753664 1755319 1756025 1757981 1764805 1767289 1779786 1836493 1864122 1870138 1876158 1909315 1912471 1936900 1945922 1954897 1961469 1972474 1981529 1983537 2027564 2062525 2077473 2086610 2091458 2095425 2159007 2161597 2163541 2168086 2177000 2186364 2189829 2193581 2248575 2274606 2287726 2290334 2291763 2292454 2309905 2356587 2363443 2406651 2415722 2431853 2455478 2455763 2463778 2501130 2519124 2562988 2618136 2619348 2718803 
15.0 5.015 2.132 4.226 4.338 0.571 0.419 0.616 0.604 8.879 1.161 3.901 1.29 1.275 4.757 0.864 4.654 14.647 3.502 6.375 1.156 9.246 0.455 0.316 0.491 2.927 0.832 1.19 0.083 0.149 1.488 2.011 0.34 5.044 7.04 2.542 3.186 3.243 2.581 12.023 0.75 0.176 3.905 1.163 2.406 2.472 3.976 3.727 3.887 0.816 2.07 0.249 0.426 4.711 1.19 4.749 4.757 4.293 2.426 7.478 3.163 2.898 1.325 0.127 0.357 0.891 2.167 17.602 6.585 2.263 1.213 7.124 32.508 2.546 10.689 6.957 0.676 11.884 11.538 2.127 1.482 1.33 2.081 1.363 1.871 5.761 1.879 2.404 2.313 7.639 4.345 1.824 1.866 25.05 5.654 0.012 0.516 3.939 0.94 4.16 11.008 19.542 2.111 1.669 0.13 3.815 11.313 2.631 1.463 2.671 5.621 2.123 4.711 1.313 1.957 2.37 13.316 8.639 2.579 2.077 5.572 3.716 21.487 4.035 0.342 2.699 2.699 9.859 32.437 11.106 4.721 2.071 0.238 1.76 0.374 2.458 6.702 8.473 8.474 7.063 7.687 3.134 4.451 0.465 1.636 3.544 0.841 3.81 5.73 5.31 2.0 2.453 2.355 5.766 2.775 2.123 13.126 5.55 4.734 4.116 3.702 6.241 9.159 4.137 2.595 2.901 9.727 3.545 0.643 6.817 0.423 5.214 0.742 3.419 0.57 1.63 4.238 0.534 13.293 1.911 8.649 7.208 0.246 1.608 0.45 5.604 0.046 0.306 0.909 2.972 7.239 1.982 3.896 2.173 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1000_0.prm:33
 Score: 101.952, AlignedPeaks: 272856 344106 472288 573305 674328 771364 868446 955393 1054485 1217500 1314684 
0 272856 286123 314162 320812 322587 326284 330005 332205 337147 343192 344106 349273 350108 355163 371155 385354 388190 389140 395260 413276 472288 504164 528209 540388 546248 548276 573305 575174 674328 675304 688144 690025 690364 710285 771364 785288 803372 821441 824448 828686 829301 848281 868446 873303 906351 908522 920550 935036 948308 955393 966336 983291 984025 1018833 1019537 1047435 1054485 1058390 1058947 1067792 1094306 1096477 1105409 1129525 1134573 1173516 1217500 1231502 1249495 1292543 1312803 1314684 1321068 1327630 1328467 1332509 1346503 1364480 1372525 1409484 1427626 1429520 1454552 1456580 1462459 1474619 1498667 1530547 1531635 1607568 1613688 1617474 1631673 1652728 1653555 1658722 1670623 1676544 1688666 1729972 1984818 
15.0 1.369 2.183 4.61 2.017 3.987 3.384 4.71 7.314 0.407 4.863 10.903 5.494 10.655 0.306 1.374 0.282 4.243 4.353 1.29 5.885 5.754 18.694 1.051 2.756 0.558 1.208 8.94 13.35 22.053 6.635 1.751 1.898 1.539 0.011 10.82 17.858 3.11 0.454 0.829 0.932 4.579 3.301 3.429 0.184 0.358 0.571 2.577 0.269 16.334 0.637 2.434 3.162 1.221 4.803 2.219 1.379 17.406 0.961 2.148 1.349 0.812 1.609 1.531 1.036 4.08 8.313 18.808 9.648 0.924 2.116 2.623 1.833 0.078 10.873 15.725 0.12 2.59 1.221 1.401 0.09 13.693 4.35 2.041 0.141 3.509 1.229 16.966 2.918 0.688 0.692 0.266 0.182 3.983 12.159 0.662 0.852 2.452 1.148 3.158 1.184 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:318
 Score: 99.259, AlignedPeaks: 445318 572974 674381 775501 872215 1056195 1155456 1318630 
0 199470 200298 216826 217999 241192 281159 286979 310171 321982 328220 346044 373429 391042 427131 443870 444718 445318 450687 451165 474263 487839 523241 569029 571946 572974 575362 597330 619358 628377 638489 641442 674381 692103 708225 709988 773414 775115 775501 785964 792021 793102 817583 819430 823631 829697 872215 890253 893744 899837 900133 900558 950350 950660 951072 975198 991944 993349 1001045 1001553 1003569 1018200 1046345 1056195 1064388 1064852 1065167 1065591 1100794 1153599 1155456 1169824 1173576 1178527 1179113 1187377 1187791 1191760 1254424 1256384 1272438 1274528 1283661 1291391 1300525 1302614 1316626 1318630 1320628 1383292 1387261 1387675 1395939 1396526 1405229 1419574 1421453 1474258 1509461 1509885 1510200 1510664 1512870 1518843 1528708 1556853 1573499 1574008 1583108 1599844 1601826 1605935 1623980 1624392 1624703 1674495 1674919 1675215 1683947 1684800 1702489 1702837 1728319 1731010 1737216 1745355 1751422 1755957 1757469 1781951 1782371 1783031 1789089 1799552 1799938 1801639 1812103 1865063 1866828 1882949 1900679 1918669 1931088 1933611 1936563 1946675 1955694 1977722 1999690 2002087 2006023 2051811 2060750 2087214 2096312 2100790 2123887 2124365 2129714 2147922 2165927 2184010 2201598 2210860 2229009 2235008 2236834 2246833 2254900 2264882 2287864 2288782 2293894 2339648 2357053 2358226 2557042 
15.0 11.047 9.218 2.158 5.651 1.582 2.557 9.021 1.705 0.53 4.516 3.345 6.886 2.406 3.403 1.492 9.277 17.808 11.794 12.835 0.849 1.079 1.731 2.322 3.498 11.344 3.557 2.855 5.115 4.854 3.743 2.121 13.609 7.568 1.211 3.205 2.682 13.918 14.59 0.463 8.497 1.495 0.796 3.21 1.725 1.491 2.618 3.747 0.6 4.053 2.03 1.492 1.949 1.192 1.328 10.994 13.943 4.254 3.338 2.735 3.014 5.191 10.215 5.438 5.624 5.791 3.259 1.786 2.164 2.535 16.179 2.477 1.535 2.042 1.796 5.098 6.093 2.313 0.112 14.538 2.319 9.645 1.996 3.562 2.684 1.298 1.014 17.673 1.767 1.412 4.747 2.337 1.795 2.516 1.277 12.698 0.952 1.283 3.906 1.704 6.473 6.453 1.343 5.453 11.15 4.047 4.544 5.806 7.674 16.82 5.754 0.628 2.577 3.213 2.799 2.795 5.316 4.358 4.657 6.45 1.673 2.75 1.816 1.634 0.618 1.822 4.59 10.042 6.122 2.589 1.216 11.894 1.768 16.089 19.967 2.792 2.214 5.295 3.614 7.599 14.916 3.696 0.165 2.278 2.66 6.027 7.18 3.713 2.3 5.614 1.426 2.467 0.457 5.003 0.456 0.827 5.153 5.097 8.034 7.42 3.365 0.042 4.159 0.331 0.405 0.518 0.574 2.061 0.126 1.605 5.348 3.205 0.658 2.201 6.024 4.347 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:752
 Score: 96.56899999999999, AlignedPeaks: 445186 573588 775297 872345 1056381 1155263 1318660 
0 127897 199271 200275 211902 228160 285480 287266 298234 392367 398774 409088 445186 464356 476072 479115 479918 512770 513500 515321 529299 559844 560317 561306 566850 573588 579383 655940 658648 677349 678022 680730 682349 685028 686381 756608 758925 761357 763183 767980 775297 776353 776826 781805 808547 817428 872345 891464 897157 909521 927662 937896 944303 957597 962455 986116 993268 994545 1006398 1035617 1049323 1056381 1108463 1155263 1155942 1187149 1190396 1318660 
15.0 0.792 8.186 22.234 0.711 6.105 0.481 5.103 5.939 0.911 0.467 5.083 11.364 5.559 0.759 2.088 1.832 3.543 3.872 2.411 0.491 2.83 3.352 12.151 3.086 6.162 1.621 0.456 0.201 3.025 3.913 0.35 0.119 1.594 4.389 0.598 2.898 1.249 5.986 5.445 13.225 6.855 7.337 1.0 1.294 2.265 6.334 4.817 0.855 2.692 5.617 0.871 0.151 0.525 1.048 0.004 0.699 0.991 2.018 0.655 4.594 17.758 2.408 11.726 4.48 1.271 4.341 15.0 

SpectrumHMM Model: * M[0] - Mass:-374170.9000000001 Overlap:4/4 LogOddsScore:8.459356596856288, SumScore:60.0, InsertsAfter: 0
 * M[1] - Mass:-174134.33333333334 Overlap:3/5 LogOddsScore:3.2351722916053958, SumScore:35.381, InsertsAfter: 7
 * M[2] - Mass:-340.8 Overlap:4/7 LogOddsScore:5.006081289134606, SumScore:38.255, InsertsAfter: 30
 * M[3] - Mass:71069.76923076922 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:186.795, InsertsAfter: 25
 * M[4] - Mass:199146.0 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:303.902, InsertsAfter: 45
 * M[5] - Mass:300198.9090909091 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:312.584, InsertsAfter: 26
 * M[6] - Mass:401222.0 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:359.362, InsertsAfter: 22
 * M[7] - Mass:498299.46153846156 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:300.289, InsertsAfter: 30
 * M[8] - Mass:595427.0 Overlap:5/7 LogOddsScore:6.760383435861036, SumScore:275.75899999999996, InsertsAfter: 27
 * M[9] - Mass:682079.5384615384 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:303.44399999999996, InsertsAfter: 37
 * M[10] - Mass:781286.6153846154 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:366.109, InsertsAfter: 25
 * M[11] - Mass:944418.3076923077 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:364.416, InsertsAfter: 52
 * M[12] - Mass:1041532.1111111111 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:277.22400000000005, InsertsAfter: 25
ConsensusPRM: -374170 -174134 -340 71069 199146 300198 401222 498299 595427 682079 781286 944418 1041532 Consensus: -374170 -174134 -340 71069 199146 300198 401222 498299 595427 682079 781286 944418 1041532
De Novo: [200.036][173.794]AKTTPPSVYP, Merged: [200.036][173.794]AKTTPPSVYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
-374170 -174134 -340 71069 199146 300198 401222 498299 595427 682079 781286 944418 1041532 1154616 1225653 1322705 1379726 1539810 1596831 1711857 1812904 1913951 1970972 2058004 2145036 2244104 2345151 2458235 2515256 2675340 2788424 2887492 3015586 3072607 3235670 3382738 3479790 3608832 3695864 3794932 3895979 3995047 4096094 4282173 4396215 4483247 4540268 4627300 4740384 4827416 4914448 5001480 5100548 5237606 5338653 5485721 5582773 5653810 5766894 5879978 6008036 6095068 6152089 6265173 6428236 6529283 6660323 6747355 6834387 6921419 7020487 7121534 7220602 7317654 7404686 7491718 7592765 7778844 7875896 7962928 8090986 8192033 8291101 8392148 8552232 8639264 8738332 8809369 8946427 9043479 9114516 9201548 9288580 9389627 9490674 9589742 9704768 9832862 9960956 10074040 10203082 10300134 10387166 10444187 10541239 10654323 10741355 10842402 10955486 11069528 11166580 11326664 11423716 11520768 11680852 11808946 11937988 12098072 12235130 12363224 12523308 12620360 12691397 12788449 12902491 13015575 13144617 13201638 13258659 13355711 13442743 13541811 13688879 13801963 13949031 14046083 14143135 14257177 14370261 14498355 14613381 14712449 14825533 14956573 15069657 15156689 15269773 15370820 15467872 15595966 15695034 15796081 15956165 
60.0 35.381 34.1275 153.39749999999998 286.951 291.29200000000003 314.68100000000004 285.1445 272.8795 286.722 318.05449999999996 317.20799999999997 273.612 270.0 270.0 270.0 270.0 255.0 255.0 300.0 300.0 270.0 330.0 315.0 330.0 285.0 300.0 345.0 330.0 390.0 510.0 540.0 585.0 360.0 405.0 405.0 405.0 645.0 690.0 765.0 1215.0 1200.0 1290.0 1515.0 1740.0 1710.0 1830.0 1845.0 1920.0 2025.0 1995.0 1965.0 1950.0 1995.0 1875.0 1770.0 1515.0 1515.0 1515.0 1200.0 945.0 480.0 480.0 435.0 450.0 255.0 240.0 225.0 195.0 240.0 240.0 240.0 225.0 225.0 225.0 225.0 225.0 225.0 225.0 195.0 195.0 150.0 120.0 180.0 330.0 345.0 330.0 360.0 360.0 375.0 375.0 375.0 390.0 390.0 375.0 375.0 450.0 1215.0 1320.0 1260.0 1365.0 1320.0 1350.0 1350.0 1350.0 1395.0 1410.0 1425.0 1335.0 1410.0 1260.0 1290.0 1290.0 1290.0 1290.0 1155.0 765.0 480.0 540.0 615.0 390.0 390.0 390.0 390.0 375.0 375.0 420.0 420.0 420.0 435.0 435.0 480.0 585.0 555.0 570.0 570.0 570.0 570.0 570.0 570.0 420.0 315.0 330.0 315.0 270.0 270.0 270.0 270.0 270.0 270.0 60.0 60.0 45.0 

(LEFT)Round: 1 for seed: [200.036][173.794]AKTTPPSVYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1250_0.prm:63
 Score: 127.71700000000001, AlignedPeaks: 0 200091 445260 573224 674298 775266 872372 969537 1056438 1155502 
0 198835 199521 200091 225963 262031 286841 356450 379187 409205 424087 427105 433303 438259 445260 451304 474035 486190 488202 520347 556315 557354 569229 573224 575296 587224 612269 622865 623291 670291 674298 731263 775266 775779 783209 793272 824451 832305 840207 872372 937268 955349 969537 973305 1008290 1008842 1026260 1031454 1045835 1056438 1121365 1125051 1137438 1155502 1218402 1236399 1254455 1286196 1318528 1320782 1329790 1367890 1368233 1368518 1381432 1392831 1399537 1411893 1415578 1418544 1480496 1491109 1528663 1563639 1567407 1581651 1599703 1635683 1663587 1664577 1668651 1696773 1704639 1712493 1725687 1743672 1753730 1761165 1761709 1779602 1797605 1826614 1862684 1913813 1914079 1924675 1961648 2109839 2127739 2157757 2180494 
15.0 1.923 1.469 2.1 6.581 2.069 1.768 2.744 3.625 3.745 5.762 5.552 4.523 3.31 12.073 1.437 5.58 5.203 3.616 8.201 4.594 5.401 5.126 9.452 1.621 0.028 1.056 3.574 8.09 1.026 12.995 1.903 27.471 8.755 5.247 3.009 2.35 1.852 3.641 6.79 19.183 9.154 0.26 0.001 17.795 1.734 0.039 1.031 0.535 8.286 2.064 0.212 2.838 18.29 16.193 2.733 1.077 2.899 17.885 3.196 2.461 1.651 0.437 2.798 16.057 1.992 5.53 0.543 1.231 1.624 6.484 0.825 18.934 1.475 0.698 3.544 20.287 0.04 2.329 3.292 0.292 7.053 1.268 0.567 1.447 0.378 6.842 21.447 19.363 2.372 1.865 2.181 1.681 3.432 1.367 2.446 1.623 2.687 0.947 1.17 1.922 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:318
 Score: 120.804, AlignedPeaks: 0 200298 445318 572974 674381 775501 872215 1056195 1155456 
0 199470 200298 216826 217999 241192 281159 286979 310171 321982 328220 346044 373429 391042 427131 443870 444718 445318 450687 451165 474263 487839 523241 569029 571946 572974 575362 597330 619358 628377 638489 641442 674381 692103 708225 709988 773414 775115 775501 785964 792021 793102 817583 819430 823631 829697 872215 890253 893744 899837 900133 900558 950350 950660 951072 975198 991944 993349 1001045 1001553 1003569 1018200 1046345 1056195 1064388 1064852 1065167 1065591 1100794 1153599 1155456 1169824 1173576 1178527 1179113 1187377 1187791 1191760 1254424 1256384 1272438 1274528 1283661 1291391 1300525 1302614 1316626 1318630 1320628 1383292 1387261 1387675 1395939 1396526 1405229 1419574 1421453 1474258 1509461 1509885 1510200 1510664 1512870 1518843 1528708 1556853 1573499 1574008 1583108 1599844 1601826 1605935 1623980 1624392 1624703 1674495 1674919 1675215 1683947 1684800 1702489 1702837 1728319 1731010 1737216 1745355 1751422 1755957 1757469 1781951 1782371 1783031 1789089 1799552 1799938 1801639 1812103 1865063 1866828 1882949 1900679 1918669 1931088 1933611 1936563 1946675 1955694 1977722 1999690 2002087 2006023 2051811 2060750 2087214 2096312 2100790 2123887 2124365 2129714 2147922 2165927 2184010 2201598 2210860 2229009 2235008 2236834 2246833 2254900 2264882 2287864 2288782 2293894 2339648 2357053 2358226 2557042 
15.0 11.047 9.218 2.158 5.651 1.582 2.557 9.021 1.705 0.53 4.516 3.345 6.886 2.406 3.403 1.492 9.277 17.808 11.794 12.835 0.849 1.079 1.731 2.322 3.498 11.344 3.557 2.855 5.115 4.854 3.743 2.121 13.609 7.568 1.211 3.205 2.682 13.918 14.59 0.463 8.497 1.495 0.796 3.21 1.725 1.491 2.618 3.747 0.6 4.053 2.03 1.492 1.949 1.192 1.328 10.994 13.943 4.254 3.338 2.735 3.014 5.191 10.215 5.438 5.624 5.791 3.259 1.786 2.164 2.535 16.179 2.477 1.535 2.042 1.796 5.098 6.093 2.313 0.112 14.538 2.319 9.645 1.996 3.562 2.684 1.298 1.014 17.673 1.767 1.412 4.747 2.337 1.795 2.516 1.277 12.698 0.952 1.283 3.906 1.704 6.473 6.453 1.343 5.453 11.15 4.047 4.544 5.806 7.674 16.82 5.754 0.628 2.577 3.213 2.799 2.795 5.316 4.358 4.657 6.45 1.673 2.75 1.816 1.634 0.618 1.822 4.59 10.042 6.122 2.589 1.216 11.894 1.768 16.089 19.967 2.792 2.214 5.295 3.614 7.599 14.916 3.696 0.165 2.278 2.66 6.027 7.18 3.713 2.3 5.614 1.426 2.467 0.457 5.003 0.456 0.827 5.153 5.097 8.034 7.42 3.365 0.042 4.159 0.331 0.405 0.518 0.574 2.061 0.126 1.605 5.348 3.205 0.658 2.201 6.024 4.347 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:752
 Score: 118.803, AlignedPeaks: 0 200275 445186 573588 775297 872345 1056381 1155263 
0 127897 199271 200275 211902 228160 285480 287266 298234 392367 398774 409088 445186 464356 476072 479115 479918 512770 513500 515321 529299 559844 560317 561306 566850 573588 579383 655940 658648 677349 678022 680730 682349 685028 686381 756608 758925 761357 763183 767980 775297 776353 776826 781805 808547 817428 872345 891464 897157 909521 927662 937896 944303 957597 962455 986116 993268 994545 1006398 1035617 1049323 1056381 1108463 1155263 1155942 1187149 1190396 1318660 
15.0 0.792 8.186 22.234 0.711 6.105 0.481 5.103 5.939 0.911 0.467 5.083 11.364 5.559 0.759 2.088 1.832 3.543 3.872 2.411 0.491 2.83 3.352 12.151 3.086 6.162 1.621 0.456 0.201 3.025 3.913 0.35 0.119 1.594 4.389 0.598 2.898 1.249 5.986 5.445 13.225 6.855 7.337 1.0 1.294 2.265 6.334 4.817 0.855 2.692 5.617 0.871 0.151 0.525 1.048 0.004 0.699 0.991 2.018 0.655 4.594 17.758 2.408 11.726 4.48 1.271 4.341 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_925_0.prm:14
 Score: 109.92699999999999, AlignedPeaks: 0 200248 445341 572929 674205 775391 872027 1056192 1155646 
0 174276 198654 200248 217962 253584 268095 275278 278469 286929 310198 320035 323356 338256 380350 394690 397396 409082 422052 424804 427157 444680 445341 463856 477498 510474 543388 565820 568911 572929 575146 587945 591534 601337 623281 623974 638465 650717 651406 668710 672290 674205 689536 708255 719463 728463 747842 757311 775391 809965 819141 846689 851491 852734 858646 862798 872027 876584 879697 885742 888308 903206 910728 913370 933226 968650 976320 1000160 1013664 1032435 1050684 1054437 1056192 1061892 1070398 1078813 1101131 1150837 1153656 1155646 1165241 1166033 1173139 1175208 1192126 1210839 1246487 1260793 1269847 1278604 1287461 1288258 1293687 1300447 1316757 1318565 1328788 1336449 1337122 1362585 1438048 1438721 1446382 1456529 1458413 1474723 1481483 1486912 1487709 1496566 1505323 1514377 1528683 1564331 1572496 1583044 1599905 1602031 1609137 1609929 1619545 1624333 1674039 1696357 1704772 1713278 1723730 1724486 1742735 1761506 1763537 1775010 1784029 1798850 1806520 1861800 1864442 1871964 1886862 1889428 1895473 1898586 1899290 1903143 1904968 1912372 1916524 1922436 1923679 1928481 1956029 1965205 1999779 2017859 2046707 2055706 2066915 2085634 2100965 2102880 2106460 2123764 2124453 2136705 2151196 2151889 2173833 2187225 2200024 2202257 2206259 2209350 2231782 2264696 2297672 2329829 2330484 2348013 2353118 2366088 2377774 2380480 2436914 2451814 2464972 2482699 2488241 2496701 2499892 2507075 2510727 2539694 2557208 2600894 2757160 
15.0 1.054 6.804 8.338 9.156 0.46 0.483 1.445 0.761 4.3 2.654 2.754 3.041 1.498 1.598 1.467 3.011 2.685 3.023 3.271 6.381 19.382 19.489 1.045 3.062 2.239 0.493 1.476 2.703 9.372 1.772 1.851 6.658 1.577 2.161 0.005 3.257 7.707 7.341 4.574 2.316 7.576 3.419 2.376 2.634 3.031 1.621 3.303 12.695 2.449 7.315 1.099 1.14 2.078 2.095 0.851 6.185 3.471 0.775 0.411 4.783 2.212 1.129 1.307 1.088 4.442 0.069 0.622 0.797 2.113 0.033 1.929 1.854 1.484 6.827 2.865 1.277 2.682 1.432 14.418 1.521 0.286 1.281 13.899 4.423 2.453 4.575 6.929 2.605 2.651 6.456 6.969 0.495 3.595 1.164 21.087 1.554 7.439 5.395 1.509 6.521 6.383 1.63 16.729 1.539 13.075 1.743 4.406 3.673 3.28 3.968 5.731 7.938 2.227 0.166 0.713 18.641 0.195 0.956 1.419 12.691 4.722 4.695 1.244 4.484 2.576 1.119 2.241 0.547 1.779 0.501 2.488 1.68 2.386 3.411 1.624 3.086 1.378 7.401 4.019 4.105 2.187 1.661 2.245 6.962 0.139 1.196 4.168 1.36 2.021 8.301 3.342 13.382 7.383 5.769 3.567 3.125 2.901 6.889 0.288 4.712 5.934 6.324 3.724 2.911 1.44 0.912 5.981 2.907 4.263 1.245 1.247 1.101 1.462 1.136 8.667 11.942 7.545 1.914 1.553 1.118 0.175 0.94 0.099 0.831 0.184 4.619 1.044 1.763 1.037 0.319 5.123 10.582 1.9 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:245
 Score: 104.694, AlignedPeaks: 0 200100 445104 573244 674333 775303 872333 1056458 1155487 
0 199478 200100 201444 234022 266965 281178 286215 286735 287129 291887 292213 294480 298005 314169 316747 373142 389077 407004 426977 445104 460130 543370 557325 573244 575304 589223 670217 674333 674775 676245 688187 731285 775303 833268 851069 868218 870201 872333 876393 932265 955404 977128 979633 1012266 1024823 1031173 1031650 1033339 1040609 1056458 1094172 1116387 1120312 1137600 1155487 1188810 1197661 1213437 1266435 1278349 1313968 1314475 1318516 1393535 1399520 1413438 1415496 1423820 1445372 1500465 1510681 1528628 1543659 1599688 1615651 1674573 1696529 1702527 1707564 1708449 1753918 1754721 1970732 
15.0 5.567 5.937 1.813 4.042 0.344 2.494 7.315 6.122 5.199 0.859 0.825 1.303 5.648 1.946 3.19 7.694 19.32 7.486 0.502 10.587 19.835 0.494 1.882 7.238 1.163 0.726 14.998 6.007 0.856 0.086 0.511 0.182 17.289 14.469 9.136 3.737 1.287 7.022 0.782 7.113 0.945 0.918 0.58 2.805 0.872 5.833 5.325 0.367 2.707 4.98 3.538 3.075 3.485 5.779 15.634 2.556 2.09 13.177 1.255 1.462 6.135 8.087 15.046 1.309 0.766 7.717 7.51 1.643 0.005 1.01 1.867 20.538 5.798 27.342 2.437 2.067 0.189 0.778 0.801 0.558 8.076 8.456 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:135.0, InsertsAfter: 0
 * M[1] - Mass:199333.00000000003 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:33.073, InsertsAfter: 3
 * M[2] - Mass:200051.58823529413 Overlap:7/7 LogOddsScore:9.96090433916431, SumScore:83.20799999999998, InsertsAfter: 0
 * M[3] - Mass:286958.43750000006 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:26.314, InsertsAfter: 19
 * M[4] - Mass:298119.5 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:11.587, InsertsAfter: 4
 * M[5] - Mass:373404.2857142858 Overlap:4/7 LogOddsScore:5.006081289134606, SumScore:48.7075, InsertsAfter: 11
 * M[6] - Mass:444699.0 Overlap:2/7 LogOddsScore:1.2992851136702874, SumScore:28.659, InsertsAfter: 22
 * M[7] - Mass:445255.294117647 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:224.71849999999998, InsertsAfter: 0
 * M[8] - Mass:573185.1176470588 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:330.519, InsertsAfter: 36
 * M[9] - Mass:674311.7857142858 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:331.47900000000004, InsertsAfter: 29
 * M[10] - Mass:775360.5882352941 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:399.951, InsertsAfter: 27
 * M[11] - Mass:872270.5294117646 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:314.0935, InsertsAfter: 29
 * M[12] - Mass:969103.5 Overlap:3/7 LogOddsScore:4.264329686730266, SumScore:277.3215, InsertsAfter: 29
 * M[13] - Mass:1056318.5882352942 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:325.03799999999995, InsertsAfter: 35
 * M[14] - Mass:1155589.7647058824 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:387.0555, InsertsAfter: 21
ConsensusPRM: 0 199333 200051 286958 298119 373404 444699 445255 573185 674311 775360 872270 969103 1056318 1155589 Consensus: 0 199333 200051 286958 298119 373404 444699 445255 573185 674311 775360 872270 969103 1056318 1155589
De Novo: [200.051]S[158.297]QTTPPSV, Merged: [200.051]SSAQTTPPSVYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
0 199333 200051 286958 298119 373404 373963 444699 445255 573185 674311 775360 872270 969103 969730 1056318 1155589 1318721 1415835 1528919 1599956 1697008 1754029 1914113 1971134 2086160 2187207 2288254 2345275 2432307 2519339 2618407 2719454 2832538 2889559 3049643 3162727 3261795 3389889 3446910 3609973 3757041 3854093 3983135 4070167 4169235 4270282 4369350 4470397 4656476 4770518 4857550 4914571 5001603 5114687 5201719 5288751 5375783 5474851 5611909 5712956 5860024 5957076 6028113 6141197 6254281 6382339 6469371 6526392 6639476 6802539 6903586 7034626 7121658 7208690 7295722 7394790 7495837 7594905 7691957 7778989 7866021 7967068 8153147 8250199 8337231 8465289 8566336 8665404 8766451 8926535 9013567 9112635 9183672 9320730 9417782 9488819 9575851 9662883 9763930 9864977 9964045 10079071 10207165 10335259 10448343 10577385 10674437 10761469 10818490 10915542 11028626 11115658 11216705 11329789 11443831 11540883 11700967 11798019 11895071 12055155 12183249 12312291 12472375 12609433 12737527 12897611 12994663 13065700 13162752 13276794 13389878 13518920 13575941 13632962 13730014 13817046 13916114 14063182 14176266 14323334 14420386 14517438 14631480 14744564 14872658 14987684 15086752 15199836 15330876 15443960 15530992 15644076 15745123 15842175 15970269 16069337 16170384 16330468 
97.5 33.073 59.29449999999999 26.314 11.587 48.7075 34.1275 28.659 189.058 308.735 311.38550000000004 357.31600000000003 299.619 277.3215 272.8795 305.88 352.55499999999995 317.20799999999997 273.612 270.0 270.0 270.0 270.0 255.0 255.0 300.0 300.0 270.0 330.0 315.0 330.0 285.0 300.0 345.0 330.0 390.0 510.0 540.0 585.0 360.0 405.0 405.0 405.0 645.0 690.0 765.0 1215.0 1200.0 1290.0 1515.0 1740.0 1710.0 1830.0 1845.0 1920.0 2025.0 1995.0 1965.0 1950.0 1995.0 1875.0 1770.0 1515.0 1515.0 1515.0 1200.0 945.0 480.0 480.0 435.0 450.0 255.0 240.0 225.0 195.0 240.0 240.0 240.0 225.0 225.0 225.0 225.0 225.0 225.0 225.0 195.0 195.0 150.0 120.0 180.0 330.0 345.0 330.0 360.0 360.0 375.0 375.0 375.0 390.0 390.0 375.0 375.0 450.0 1215.0 1320.0 1260.0 1365.0 1320.0 1350.0 1350.0 1350.0 1395.0 1410.0 1425.0 1335.0 1410.0 1260.0 1290.0 1290.0 1290.0 1290.0 1155.0 765.0 480.0 540.0 615.0 390.0 390.0 390.0 390.0 375.0 375.0 420.0 420.0 420.0 435.0 435.0 480.0 585.0 555.0 570.0 570.0 570.0 570.0 570.0 570.0 420.0 315.0 330.0 315.0 270.0 270.0 270.0 270.0 270.0 270.0 60.0 60.0 45.0 

(LEFT)Round: 2 for seed: [200.051]SSAQTTPPSVYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:318
 Score: 113.646, AlignedPeaks: 0 200298 286979 445318 572974 674381 775501 872215 1056195 
0 199470 200298 216826 217999 241192 281159 286979 310171 321982 328220 346044 373429 391042 427131 443870 444718 445318 450687 451165 474263 487839 523241 569029 571946 572974 575362 597330 619358 628377 638489 641442 674381 692103 708225 709988 773414 775115 775501 785964 792021 793102 817583 819430 823631 829697 872215 890253 893744 899837 900133 900558 950350 950660 951072 975198 991944 993349 1001045 1001553 1003569 1018200 1046345 1056195 1064388 1064852 1065167 1065591 1100794 1153599 1155456 1169824 1173576 1178527 1179113 1187377 1187791 1191760 1254424 1256384 1272438 1274528 1283661 1291391 1300525 1302614 1316626 1318630 1320628 1383292 1387261 1387675 1395939 1396526 1405229 1419574 1421453 1474258 1509461 1509885 1510200 1510664 1512870 1518843 1528708 1556853 1573499 1574008 1583108 1599844 1601826 1605935 1623980 1624392 1624703 1674495 1674919 1675215 1683947 1684800 1702489 1702837 1728319 1731010 1737216 1745355 1751422 1755957 1757469 1781951 1782371 1783031 1789089 1799552 1799938 1801639 1812103 1865063 1866828 1882949 1900679 1918669 1931088 1933611 1936563 1946675 1955694 1977722 1999690 2002087 2006023 2051811 2060750 2087214 2096312 2100790 2123887 2124365 2129714 2147922 2165927 2184010 2201598 2210860 2229009 2235008 2236834 2246833 2254900 2264882 2287864 2288782 2293894 2339648 2357053 2358226 2557042 
15.0 11.047 9.218 2.158 5.651 1.582 2.557 9.021 1.705 0.53 4.516 3.345 6.886 2.406 3.403 1.492 9.277 17.808 11.794 12.835 0.849 1.079 1.731 2.322 3.498 11.344 3.557 2.855 5.115 4.854 3.743 2.121 13.609 7.568 1.211 3.205 2.682 13.918 14.59 0.463 8.497 1.495 0.796 3.21 1.725 1.491 2.618 3.747 0.6 4.053 2.03 1.492 1.949 1.192 1.328 10.994 13.943 4.254 3.338 2.735 3.014 5.191 10.215 5.438 5.624 5.791 3.259 1.786 2.164 2.535 16.179 2.477 1.535 2.042 1.796 5.098 6.093 2.313 0.112 14.538 2.319 9.645 1.996 3.562 2.684 1.298 1.014 17.673 1.767 1.412 4.747 2.337 1.795 2.516 1.277 12.698 0.952 1.283 3.906 1.704 6.473 6.453 1.343 5.453 11.15 4.047 4.544 5.806 7.674 16.82 5.754 0.628 2.577 3.213 2.799 2.795 5.316 4.358 4.657 6.45 1.673 2.75 1.816 1.634 0.618 1.822 4.59 10.042 6.122 2.589 1.216 11.894 1.768 16.089 19.967 2.792 2.214 5.295 3.614 7.599 14.916 3.696 0.165 2.278 2.66 6.027 7.18 3.713 2.3 5.614 1.426 2.467 0.457 5.003 0.456 0.827 5.153 5.097 8.034 7.42 3.365 0.042 4.159 0.331 0.405 0.518 0.574 2.061 0.126 1.605 5.348 3.205 0.658 2.201 6.024 4.347 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:752
 Score: 112.18, AlignedPeaks: 0 200275 287266 445186 573588 775297 872345 1056381 
0 127897 199271 200275 211902 228160 285480 287266 298234 392367 398774 409088 445186 464356 476072 479115 479918 512770 513500 515321 529299 559844 560317 561306 566850 573588 579383 655940 658648 677349 678022 680730 682349 685028 686381 756608 758925 761357 763183 767980 775297 776353 776826 781805 808547 817428 872345 891464 897157 909521 927662 937896 944303 957597 962455 986116 993268 994545 1006398 1035617 1049323 1056381 1108463 1155263 1155942 1187149 1190396 1318660 
15.0 0.792 8.186 22.234 0.711 6.105 0.481 5.103 5.939 0.911 0.467 5.083 11.364 5.559 0.759 2.088 1.832 3.543 3.872 2.411 0.491 2.83 3.352 12.151 3.086 6.162 1.621 0.456 0.201 3.025 3.913 0.35 0.119 1.594 4.389 0.598 2.898 1.249 5.986 5.445 13.225 6.855 7.337 1.0 1.294 2.265 6.334 4.817 0.855 2.692 5.617 0.871 0.151 0.525 1.048 0.004 0.699 0.991 2.018 0.655 4.594 17.758 2.408 11.726 4.48 1.271 4.341 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1250_0.prm:63
 Score: 111.19500000000001, AlignedPeaks: 0 200091 286841 445260 573224 674298 775266 872372 969537 1056438 
0 198835 199521 200091 225963 262031 286841 356450 379187 409205 424087 427105 433303 438259 445260 451304 474035 486190 488202 520347 556315 557354 569229 573224 575296 587224 612269 622865 623291 670291 674298 731263 775266 775779 783209 793272 824451 832305 840207 872372 937268 955349 969537 973305 1008290 1008842 1026260 1031454 1045835 1056438 1121365 1125051 1137438 1155502 1218402 1236399 1254455 1286196 1318528 1320782 1329790 1367890 1368233 1368518 1381432 1392831 1399537 1411893 1415578 1418544 1480496 1491109 1528663 1563639 1567407 1581651 1599703 1635683 1663587 1664577 1668651 1696773 1704639 1712493 1725687 1743672 1753730 1761165 1761709 1779602 1797605 1826614 1862684 1913813 1914079 1924675 1961648 2109839 2127739 2157757 2180494 
15.0 1.923 1.469 2.1 6.581 2.069 1.768 2.744 3.625 3.745 5.762 5.552 4.523 3.31 12.073 1.437 5.58 5.203 3.616 8.201 4.594 5.401 5.126 9.452 1.621 0.028 1.056 3.574 8.09 1.026 12.995 1.903 27.471 8.755 5.247 3.009 2.35 1.852 3.641 6.79 19.183 9.154 0.26 0.001 17.795 1.734 0.039 1.031 0.535 8.286 2.064 0.212 2.838 18.29 16.193 2.733 1.077 2.899 17.885 3.196 2.461 1.651 0.437 2.798 16.057 1.992 5.53 0.543 1.231 1.624 6.484 0.825 18.934 1.475 0.698 3.544 20.287 0.04 2.329 3.292 0.292 7.053 1.268 0.567 1.447 0.378 6.842 21.447 19.363 2.372 1.865 2.181 1.681 3.432 1.367 2.446 1.623 2.687 0.947 1.17 1.922 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_925_0.prm:14
 Score: 104.25100000000002, AlignedPeaks: 0 200248 286929 445341 572929 674205 775391 872027 968650 1056192 
0 174276 198654 200248 217962 253584 268095 275278 278469 286929 310198 320035 323356 338256 380350 394690 397396 409082 422052 424804 427157 444680 445341 463856 477498 510474 543388 565820 568911 572929 575146 587945 591534 601337 623281 623974 638465 650717 651406 668710 672290 674205 689536 708255 719463 728463 747842 757311 775391 809965 819141 846689 851491 852734 858646 862798 872027 876584 879697 885742 888308 903206 910728 913370 933226 968650 976320 1000160 1013664 1032435 1050684 1054437 1056192 1061892 1070398 1078813 1101131 1150837 1153656 1155646 1165241 1166033 1173139 1175208 1192126 1210839 1246487 1260793 1269847 1278604 1287461 1288258 1293687 1300447 1316757 1318565 1328788 1336449 1337122 1362585 1438048 1438721 1446382 1456529 1458413 1474723 1481483 1486912 1487709 1496566 1505323 1514377 1528683 1564331 1572496 1583044 1599905 1602031 1609137 1609929 1619545 1624333 1674039 1696357 1704772 1713278 1723730 1724486 1742735 1761506 1763537 1775010 1784029 1798850 1806520 1861800 1864442 1871964 1886862 1889428 1895473 1898586 1899290 1903143 1904968 1912372 1916524 1922436 1923679 1928481 1956029 1965205 1999779 2017859 2046707 2055706 2066915 2085634 2100965 2102880 2106460 2123764 2124453 2136705 2151196 2151889 2173833 2187225 2200024 2202257 2206259 2209350 2231782 2264696 2297672 2329829 2330484 2348013 2353118 2366088 2377774 2380480 2436914 2451814 2464972 2482699 2488241 2496701 2499892 2507075 2510727 2539694 2557208 2600894 2757160 
15.0 1.054 6.804 8.338 9.156 0.46 0.483 1.445 0.761 4.3 2.654 2.754 3.041 1.498 1.598 1.467 3.011 2.685 3.023 3.271 6.381 19.382 19.489 1.045 3.062 2.239 0.493 1.476 2.703 9.372 1.772 1.851 6.658 1.577 2.161 0.005 3.257 7.707 7.341 4.574 2.316 7.576 3.419 2.376 2.634 3.031 1.621 3.303 12.695 2.449 7.315 1.099 1.14 2.078 2.095 0.851 6.185 3.471 0.775 0.411 4.783 2.212 1.129 1.307 1.088 4.442 0.069 0.622 0.797 2.113 0.033 1.929 1.854 1.484 6.827 2.865 1.277 2.682 1.432 14.418 1.521 0.286 1.281 13.899 4.423 2.453 4.575 6.929 2.605 2.651 6.456 6.969 0.495 3.595 1.164 21.087 1.554 7.439 5.395 1.509 6.521 6.383 1.63 16.729 1.539 13.075 1.743 4.406 3.673 3.28 3.968 5.731 7.938 2.227 0.166 0.713 18.641 0.195 0.956 1.419 12.691 4.722 4.695 1.244 4.484 2.576 1.119 2.241 0.547 1.779 0.501 2.488 1.68 2.386 3.411 1.624 3.086 1.378 7.401 4.019 4.105 2.187 1.661 2.245 6.962 0.139 1.196 4.168 1.36 2.021 8.301 3.342 13.382 7.383 5.769 3.567 3.125 2.901 6.889 0.288 4.712 5.934 6.324 3.724 2.911 1.44 0.912 5.981 2.907 4.263 1.245 1.247 1.101 1.462 1.136 8.667 11.942 7.545 1.914 1.553 1.118 0.175 0.94 0.099 0.831 0.184 4.619 1.044 1.763 1.037 0.319 5.123 10.582 1.9 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:245
 Score: 95.18200000000002, AlignedPeaks: 0 200100 286735 445104 573244 674333 775303 872333 1056458 
0 199478 200100 201444 234022 266965 281178 286215 286735 287129 291887 292213 294480 298005 314169 316747 373142 389077 407004 426977 445104 460130 543370 557325 573244 575304 589223 670217 674333 674775 676245 688187 731285 775303 833268 851069 868218 870201 872333 876393 932265 955404 977128 979633 1012266 1024823 1031173 1031650 1033339 1040609 1056458 1094172 1116387 1120312 1137600 1155487 1188810 1197661 1213437 1266435 1278349 1313968 1314475 1318516 1393535 1399520 1413438 1415496 1423820 1445372 1500465 1510681 1528628 1543659 1599688 1615651 1674573 1696529 1702527 1707564 1708449 1753918 1754721 1970732 
15.0 5.567 5.937 1.813 4.042 0.344 2.494 7.315 6.122 5.199 0.859 0.825 1.303 5.648 1.946 3.19 7.694 19.32 7.486 0.502 10.587 19.835 0.494 1.882 7.238 1.163 0.726 14.998 6.007 0.856 0.086 0.511 0.182 17.289 14.469 9.136 3.737 1.287 7.022 0.782 7.113 0.945 0.918 0.58 2.805 0.872 5.833 5.325 0.367 2.707 4.98 3.538 3.075 3.485 5.779 15.634 2.556 2.09 13.177 1.255 1.462 6.135 8.087 15.046 1.309 0.766 7.717 7.51 1.643 0.005 1.01 1.867 20.538 5.798 27.342 2.437 2.067 0.189 0.778 0.801 0.558 8.076 8.456 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:172.5, InsertsAfter: 0
 * M[1] - Mass:199333.00000000003 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:33.073, InsertsAfter: 3
 * M[2] - Mass:200088.73333333334 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:107.12149999999998, InsertsAfter: 0
 * M[3] - Mass:286964.86666666664 Overlap:7/7 LogOddsScore:8.750161912830762, SumScore:52.628, InsertsAfter: 19
 * M[4] - Mass:298119.5 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:11.587, InsertsAfter: 4
 * M[5] - Mass:373422.33333333326 Overlap:4/7 LogOddsScore:5.006081289134606, SumScore:48.7075, InsertsAfter: 11
 * M[6] - Mass:444699.0 Overlap:2/7 LogOddsScore:1.2992851136702874, SumScore:28.659, InsertsAfter: 22
 * M[7] - Mass:445251.86666666664 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:260.379, InsertsAfter: 0
 * M[8] - Mass:573187.8666666667 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:352.303, InsertsAfter: 36
 * M[9] - Mass:674302.4166666667 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:351.57250000000005, InsertsAfter: 29
 * M[10] - Mass:775355.4000000003 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:442.586, InsertsAfter: 27
 * M[11] - Mass:872254.2 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:328.56800000000004, InsertsAfter: 29
 * M[12] - Mass:968763.25 Overlap:3/7 LogOddsScore:4.264329686730266, SumScore:281.7635, InsertsAfter: 29
 * M[13] - Mass:1056323.4666666668 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:344.19599999999997, InsertsAfter: 35
ConsensusPRM: 0 199333 200088 286964 298119 373422 444699 445251 573187 674302 775355 872254 968763 1056323 Consensus: 0 199333 200088 286964 298119 373422 444699 445251 573187 674302 775355 872254 968763 1056323
De Novo: [200.088]S[158.287]QTTP[184.069], Merged: [200.088]SSAQTTP[184.069]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
0 199333 200088 286964 298119 373422 373968 444699 445251 573187 674302 775355 872254 968763 1056323 1155594 1318726 1415840 1528924 1599961 1697013 1754034 1914118 1971139 2086165 2187212 2288259 2345280 2432312 2519344 2618412 2719459 2832543 2889564 3049648 3162732 3261800 3389894 3446915 3609978 3757046 3854098 3983140 4070172 4169240 4270287 4369355 4470402 4656481 4770523 4857555 4914576 5001608 5114692 5201724 5288756 5375788 5474856 5611914 5712961 5860029 5957081 6028118 6141202 6254286 6382344 6469376 6526397 6639481 6802544 6903591 7034631 7121663 7208695 7295727 7394795 7495842 7594910 7691962 7778994 7866026 7967073 8153152 8250204 8337236 8465294 8566341 8665409 8766456 8926540 9013572 9112640 9183677 9320735 9417787 9488824 9575856 9662888 9763935 9864982 9964050 10079076 10207170 10335264 10448348 10577390 10674442 10761474 10818495 10915547 11028631 11115663 11216710 11329794 11443836 11540888 11700972 11798024 11895076 12055160 12183254 12312296 12472380 12609438 12737532 12897616 12994668 13065705 13162757 13276799 13389883 13518925 13575946 13632967 13730019 13817051 13916119 14063187 14176271 14323339 14420391 14517443 14631485 14744569 14872663 14987689 15086757 15199841 15330881 15443965 15530997 15644081 15745128 15842180 15970274 16069342 16170389 16330473 
135.0 33.073 83.20799999999998 39.471000000000004 11.587 48.7075 34.1275 28.659 224.7185 330.519 331.47900000000004 399.951 314.09350000000006 279.5425 325.038 352.55499999999995 317.20799999999997 273.612 270.0 270.0 270.0 270.0 255.0 255.0 300.0 300.0 270.0 330.0 315.0 330.0 285.0 300.0 345.0 330.0 390.0 510.0 540.0 585.0 360.0 405.0 405.0 405.0 645.0 690.0 765.0 1215.0 1200.0 1290.0 1515.0 1740.0 1710.0 1830.0 1845.0 1920.0 2025.0 1995.0 1965.0 1950.0 1995.0 1875.0 1770.0 1515.0 1515.0 1515.0 1200.0 945.0 480.0 480.0 435.0 450.0 255.0 240.0 225.0 195.0 240.0 240.0 240.0 225.0 225.0 225.0 225.0 225.0 225.0 225.0 195.0 195.0 150.0 120.0 180.0 330.0 345.0 330.0 360.0 360.0 375.0 375.0 375.0 390.0 390.0 375.0 375.0 450.0 1215.0 1320.0 1260.0 1365.0 1320.0 1350.0 1350.0 1350.0 1395.0 1410.0 1425.0 1335.0 1410.0 1260.0 1290.0 1290.0 1290.0 1290.0 1155.0 765.0 480.0 540.0 615.0 390.0 390.0 390.0 390.0 375.0 375.0 420.0 420.0 420.0 435.0 435.0 480.0 585.0 555.0 570.0 570.0 570.0 570.0 570.0 570.0 420.0 315.0 330.0 315.0 270.0 270.0 270.0 270.0 270.0 270.0 60.0 60.0 45.0 

(LEFT)Round: 3 for seed: [200.088]SSAQTTP[184.069]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:318
 Score: 129.825, AlignedPeaks: 0 200298 286979 445318 572974 674381 775501 872215 1056195 1155456 
0 199470 200298 216826 217999 241192 281159 286979 310171 321982 328220 346044 373429 391042 427131 443870 444718 445318 450687 451165 474263 487839 523241 569029 571946 572974 575362 597330 619358 628377 638489 641442 674381 692103 708225 709988 773414 775115 775501 785964 792021 793102 817583 819430 823631 829697 872215 890253 893744 899837 900133 900558 950350 950660 951072 975198 991944 993349 1001045 1001553 1003569 1018200 1046345 1056195 1064388 1064852 1065167 1065591 1100794 1153599 1155456 1169824 1173576 1178527 1179113 1187377 1187791 1191760 1254424 1256384 1272438 1274528 1283661 1291391 1300525 1302614 1316626 1318630 1320628 1383292 1387261 1387675 1395939 1396526 1405229 1419574 1421453 1474258 1509461 1509885 1510200 1510664 1512870 1518843 1528708 1556853 1573499 1574008 1583108 1599844 1601826 1605935 1623980 1624392 1624703 1674495 1674919 1675215 1683947 1684800 1702489 1702837 1728319 1731010 1737216 1745355 1751422 1755957 1757469 1781951 1782371 1783031 1789089 1799552 1799938 1801639 1812103 1865063 1866828 1882949 1900679 1918669 1931088 1933611 1936563 1946675 1955694 1977722 1999690 2002087 2006023 2051811 2060750 2087214 2096312 2100790 2123887 2124365 2129714 2147922 2165927 2184010 2201598 2210860 2229009 2235008 2236834 2246833 2254900 2264882 2287864 2288782 2293894 2339648 2357053 2358226 2557042 
15.0 11.047 9.218 2.158 5.651 1.582 2.557 9.021 1.705 0.53 4.516 3.345 6.886 2.406 3.403 1.492 9.277 17.808 11.794 12.835 0.849 1.079 1.731 2.322 3.498 11.344 3.557 2.855 5.115 4.854 3.743 2.121 13.609 7.568 1.211 3.205 2.682 13.918 14.59 0.463 8.497 1.495 0.796 3.21 1.725 1.491 2.618 3.747 0.6 4.053 2.03 1.492 1.949 1.192 1.328 10.994 13.943 4.254 3.338 2.735 3.014 5.191 10.215 5.438 5.624 5.791 3.259 1.786 2.164 2.535 16.179 2.477 1.535 2.042 1.796 5.098 6.093 2.313 0.112 14.538 2.319 9.645 1.996 3.562 2.684 1.298 1.014 17.673 1.767 1.412 4.747 2.337 1.795 2.516 1.277 12.698 0.952 1.283 3.906 1.704 6.473 6.453 1.343 5.453 11.15 4.047 4.544 5.806 7.674 16.82 5.754 0.628 2.577 3.213 2.799 2.795 5.316 4.358 4.657 6.45 1.673 2.75 1.816 1.634 0.618 1.822 4.59 10.042 6.122 2.589 1.216 11.894 1.768 16.089 19.967 2.792 2.214 5.295 3.614 7.599 14.916 3.696 0.165 2.278 2.66 6.027 7.18 3.713 2.3 5.614 1.426 2.467 0.457 5.003 0.456 0.827 5.153 5.097 8.034 7.42 3.365 0.042 4.159 0.331 0.405 0.518 0.574 2.061 0.126 1.605 5.348 3.205 0.658 2.201 6.024 4.347 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1250_0.prm:63
 Score: 129.225, AlignedPeaks: 0 200091 286841 445260 573224 674298 775266 872372 1056438 1155502 
0 198835 199521 200091 225963 262031 286841 356450 379187 409205 424087 427105 433303 438259 445260 451304 474035 486190 488202 520347 556315 557354 569229 573224 575296 587224 612269 622865 623291 670291 674298 731263 775266 775779 783209 793272 824451 832305 840207 872372 937268 955349 969537 973305 1008290 1008842 1026260 1031454 1045835 1056438 1121365 1125051 1137438 1155502 1218402 1236399 1254455 1286196 1318528 1320782 1329790 1367890 1368233 1368518 1381432 1392831 1399537 1411893 1415578 1418544 1480496 1491109 1528663 1563639 1567407 1581651 1599703 1635683 1663587 1664577 1668651 1696773 1704639 1712493 1725687 1743672 1753730 1761165 1761709 1779602 1797605 1826614 1862684 1913813 1914079 1924675 1961648 2109839 2127739 2157757 2180494 
15.0 1.923 1.469 2.1 6.581 2.069 1.768 2.744 3.625 3.745 5.762 5.552 4.523 3.31 12.073 1.437 5.58 5.203 3.616 8.201 4.594 5.401 5.126 9.452 1.621 0.028 1.056 3.574 8.09 1.026 12.995 1.903 27.471 8.755 5.247 3.009 2.35 1.852 3.641 6.79 19.183 9.154 0.26 0.001 17.795 1.734 0.039 1.031 0.535 8.286 2.064 0.212 2.838 18.29 16.193 2.733 1.077 2.899 17.885 3.196 2.461 1.651 0.437 2.798 16.057 1.992 5.53 0.543 1.231 1.624 6.484 0.825 18.934 1.475 0.698 3.544 20.287 0.04 2.329 3.292 0.292 7.053 1.268 0.567 1.447 0.378 6.842 21.447 19.363 2.372 1.865 2.181 1.681 3.432 1.367 2.446 1.623 2.687 0.947 1.17 1.922 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:752
 Score: 123.906, AlignedPeaks: 0 200275 287266 445186 573588 775297 872345 1056381 1155263 
0 127897 199271 200275 211902 228160 285480 287266 298234 392367 398774 409088 445186 464356 476072 479115 479918 512770 513500 515321 529299 559844 560317 561306 566850 573588 579383 655940 658648 677349 678022 680730 682349 685028 686381 756608 758925 761357 763183 767980 775297 776353 776826 781805 808547 817428 872345 891464 897157 909521 927662 937896 944303 957597 962455 986116 993268 994545 1006398 1035617 1049323 1056381 1108463 1155263 1155942 1187149 1190396 1318660 
15.0 0.792 8.186 22.234 0.711 6.105 0.481 5.103 5.939 0.911 0.467 5.083 11.364 5.559 0.759 2.088 1.832 3.543 3.872 2.411 0.491 2.83 3.352 12.151 3.086 6.162 1.621 0.456 0.201 3.025 3.913 0.35 0.119 1.594 4.389 0.598 2.898 1.249 5.986 5.445 13.225 6.855 7.337 1.0 1.294 2.265 6.334 4.817 0.855 2.692 5.617 0.871 0.151 0.525 1.048 0.004 0.699 0.991 2.018 0.655 4.594 17.758 2.408 11.726 4.48 1.271 4.341 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_925_0.prm:14
 Score: 114.227, AlignedPeaks: 0 200248 286929 445341 572929 674205 775391 872027 1056192 1155646 
0 174276 198654 200248 217962 253584 268095 275278 278469 286929 310198 320035 323356 338256 380350 394690 397396 409082 422052 424804 427157 444680 445341 463856 477498 510474 543388 565820 568911 572929 575146 587945 591534 601337 623281 623974 638465 650717 651406 668710 672290 674205 689536 708255 719463 728463 747842 757311 775391 809965 819141 846689 851491 852734 858646 862798 872027 876584 879697 885742 888308 903206 910728 913370 933226 968650 976320 1000160 1013664 1032435 1050684 1054437 1056192 1061892 1070398 1078813 1101131 1150837 1153656 1155646 1165241 1166033 1173139 1175208 1192126 1210839 1246487 1260793 1269847 1278604 1287461 1288258 1293687 1300447 1316757 1318565 1328788 1336449 1337122 1362585 1438048 1438721 1446382 1456529 1458413 1474723 1481483 1486912 1487709 1496566 1505323 1514377 1528683 1564331 1572496 1583044 1599905 1602031 1609137 1609929 1619545 1624333 1674039 1696357 1704772 1713278 1723730 1724486 1742735 1761506 1763537 1775010 1784029 1798850 1806520 1861800 1864442 1871964 1886862 1889428 1895473 1898586 1899290 1903143 1904968 1912372 1916524 1922436 1923679 1928481 1956029 1965205 1999779 2017859 2046707 2055706 2066915 2085634 2100965 2102880 2106460 2123764 2124453 2136705 2151196 2151889 2173833 2187225 2200024 2202257 2206259 2209350 2231782 2264696 2297672 2329829 2330484 2348013 2353118 2366088 2377774 2380480 2436914 2451814 2464972 2482699 2488241 2496701 2499892 2507075 2510727 2539694 2557208 2600894 2757160 
15.0 1.054 6.804 8.338 9.156 0.46 0.483 1.445 0.761 4.3 2.654 2.754 3.041 1.498 1.598 1.467 3.011 2.685 3.023 3.271 6.381 19.382 19.489 1.045 3.062 2.239 0.493 1.476 2.703 9.372 1.772 1.851 6.658 1.577 2.161 0.005 3.257 7.707 7.341 4.574 2.316 7.576 3.419 2.376 2.634 3.031 1.621 3.303 12.695 2.449 7.315 1.099 1.14 2.078 2.095 0.851 6.185 3.471 0.775 0.411 4.783 2.212 1.129 1.307 1.088 4.442 0.069 0.622 0.797 2.113 0.033 1.929 1.854 1.484 6.827 2.865 1.277 2.682 1.432 14.418 1.521 0.286 1.281 13.899 4.423 2.453 4.575 6.929 2.605 2.651 6.456 6.969 0.495 3.595 1.164 21.087 1.554 7.439 5.395 1.509 6.521 6.383 1.63 16.729 1.539 13.075 1.743 4.406 3.673 3.28 3.968 5.731 7.938 2.227 0.166 0.713 18.641 0.195 0.956 1.419 12.691 4.722 4.695 1.244 4.484 2.576 1.119 2.241 0.547 1.779 0.501 2.488 1.68 2.386 3.411 1.624 3.086 1.378 7.401 4.019 4.105 2.187 1.661 2.245 6.962 0.139 1.196 4.168 1.36 2.021 8.301 3.342 13.382 7.383 5.769 3.567 3.125 2.901 6.889 0.288 4.712 5.934 6.324 3.724 2.911 1.44 0.912 5.981 2.907 4.263 1.245 1.247 1.101 1.462 1.136 8.667 11.942 7.545 1.914 1.553 1.118 0.175 0.94 0.099 0.831 0.184 4.619 1.044 1.763 1.037 0.319 5.123 10.582 1.9 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:245
 Score: 110.81600000000002, AlignedPeaks: 0 200100 286735 445104 573244 674333 775303 872333 1056458 1155487 
0 199478 200100 201444 234022 266965 281178 286215 286735 287129 291887 292213 294480 298005 314169 316747 373142 389077 407004 426977 445104 460130 543370 557325 573244 575304 589223 670217 674333 674775 676245 688187 731285 775303 833268 851069 868218 870201 872333 876393 932265 955404 977128 979633 1012266 1024823 1031173 1031650 1033339 1040609 1056458 1094172 1116387 1120312 1137600 1155487 1188810 1197661 1213437 1266435 1278349 1313968 1314475 1318516 1393535 1399520 1413438 1415496 1423820 1445372 1500465 1510681 1528628 1543659 1599688 1615651 1674573 1696529 1702527 1707564 1708449 1753918 1754721 1970732 
15.0 5.567 5.937 1.813 4.042 0.344 2.494 7.315 6.122 5.199 0.859 0.825 1.303 5.648 1.946 3.19 7.694 19.32 7.486 0.502 10.587 19.835 0.494 1.882 7.238 1.163 0.726 14.998 6.007 0.856 0.086 0.511 0.182 17.289 14.469 9.136 3.737 1.287 7.022 0.782 7.113 0.945 0.918 0.58 2.805 0.872 5.833 5.325 0.367 2.707 4.98 3.538 3.075 3.485 5.779 15.634 2.556 2.09 13.177 1.255 1.462 6.135 8.087 15.046 1.309 0.766 7.717 7.51 1.643 0.005 1.01 1.867 20.538 5.798 27.342 2.437 2.067 0.189 0.778 0.801 0.558 8.076 8.456 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:210.0, InsertsAfter: 0
 * M[1] - Mass:199333.00000000003 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:33.073, InsertsAfter: 3
 * M[2] - Mass:200091.20000000004 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:131.035, InsertsAfter: 0
 * M[3] - Mass:286965.2666666668 Overlap:7/7 LogOddsScore:8.750161912830762, SumScore:65.785, InsertsAfter: 19
 * M[4] - Mass:298119.5 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:11.587, InsertsAfter: 4
 * M[5] - Mass:373423.1666666666 Overlap:4/7 LogOddsScore:5.006081289134606, SumScore:48.7075, InsertsAfter: 11
 * M[6] - Mass:444699.0 Overlap:2/7 LogOddsScore:1.2992851136702874, SumScore:28.659, InsertsAfter: 22
 * M[7] - Mass:445251.6 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:296.0395, InsertsAfter: 0
 * M[8] - Mass:573188.0 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:374.087, InsertsAfter: 36
 * M[9] - Mass:674301.6666666667 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:371.66600000000005, InsertsAfter: 29
 * M[10] - Mass:775355.0666666668 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:485.221, InsertsAfter: 27
 * M[11] - Mass:872253.1333333333 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:343.0425000000001, InsertsAfter: 29
 * M[12] - Mass:1056323.8000000003 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:363.354, InsertsAfter: 65
 * M[13] - Mass:1155613.7333333334 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:421.556, InsertsAfter: 21
ConsensusPRM: 0 199333 200091 286965 298119 373423 444699 445251 573188 674301 775355 872253 1056323 1155613 Consensus: 0 199333 200091 286965 298119 373423 444699 445251 573188 674301 775355 872253 1056323 1155613
De Novo: [200.091]S[158.286]QTTP[184.07]V, Merged: [200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
0 199333 200091 286965 298119 373423 373987 444699 445251 573188 674301 775355 872253 1056323 1155613 1318745 1415859 1528943 1599980 1697032 1754053 1914137 1971158 2086184 2187231 2288278 2345299 2432331 2519363 2618431 2719478 2832562 2889583 3049667 3162751 3261819 3389913 3446934 3609997 3757065 3854117 3983159 4070191 4169259 4270306 4369374 4470421 4656500 4770542 4857574 4914595 5001627 5114711 5201743 5288775 5375807 5474875 5611933 5712980 5860048 5957100 6028137 6141221 6254305 6382363 6469395 6526416 6639500 6802563 6903610 7034650 7121682 7208714 7295746 7394814 7495861 7594929 7691981 7779013 7866045 7967092 8153171 8250223 8337255 8465313 8566360 8665428 8766475 8926559 9013591 9112659 9183696 9320754 9417806 9488843 9575875 9662907 9763954 9865001 9964069 10079095 10207189 10335283 10448367 10577409 10674461 10761493 10818514 10915566 11028650 11115682 11216729 11329813 11443855 11540907 11700991 11798043 11895095 12055179 12183273 12312315 12472399 12609457 12737551 12897635 12994687 13065724 13162776 13276818 13389902 13518944 13575965 13632986 13730038 13817070 13916138 14063206 14176290 14323358 14420410 14517462 14631504 14744588 14872682 14987708 15086776 15199860 15330900 15443984 15531016 15644100 15745147 15842199 15970293 16069361 16170408 16330492 
172.5 33.073 107.1215 52.628 11.587 48.7075 34.1275 28.659 260.379 352.303 351.57250000000005 442.586 328.5680000000001 344.196 387.05549999999994 317.20799999999997 273.612 270.0 270.0 270.0 270.0 255.0 255.0 300.0 300.0 270.0 330.0 315.0 330.0 285.0 300.0 345.0 330.0 390.0 510.0 540.0 585.0 360.0 405.0 405.0 405.0 645.0 690.0 765.0 1215.0 1200.0 1290.0 1515.0 1740.0 1710.0 1830.0 1845.0 1920.0 2025.0 1995.0 1965.0 1950.0 1995.0 1875.0 1770.0 1515.0 1515.0 1515.0 1200.0 945.0 480.0 480.0 435.0 450.0 255.0 240.0 225.0 195.0 240.0 240.0 240.0 225.0 225.0 225.0 225.0 225.0 225.0 225.0 195.0 195.0 150.0 120.0 180.0 330.0 345.0 330.0 360.0 360.0 375.0 375.0 375.0 390.0 390.0 375.0 375.0 450.0 1215.0 1320.0 1260.0 1365.0 1320.0 1350.0 1350.0 1350.0 1395.0 1410.0 1425.0 1335.0 1410.0 1260.0 1290.0 1290.0 1290.0 1290.0 1155.0 765.0 480.0 540.0 615.0 390.0 390.0 390.0 390.0 375.0 375.0 420.0 420.0 420.0 435.0 435.0 480.0 585.0 555.0 570.0 570.0 570.0 570.0 570.0 570.0 420.0 315.0 330.0 315.0 270.0 270.0 270.0 270.0 270.0 270.0 60.0 60.0 45.0 

(LEFT)Round: 4 for seed: [200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:318
 Score: 129.825, AlignedPeaks: 0 200298 286979 445318 572974 674381 775501 872215 1056195 1155456 
0 199470 200298 216826 217999 241192 281159 286979 310171 321982 328220 346044 373429 391042 427131 443870 444718 445318 450687 451165 474263 487839 523241 569029 571946 572974 575362 597330 619358 628377 638489 641442 674381 692103 708225 709988 773414 775115 775501 785964 792021 793102 817583 819430 823631 829697 872215 890253 893744 899837 900133 900558 950350 950660 951072 975198 991944 993349 1001045 1001553 1003569 1018200 1046345 1056195 1064388 1064852 1065167 1065591 1100794 1153599 1155456 1169824 1173576 1178527 1179113 1187377 1187791 1191760 1254424 1256384 1272438 1274528 1283661 1291391 1300525 1302614 1316626 1318630 1320628 1383292 1387261 1387675 1395939 1396526 1405229 1419574 1421453 1474258 1509461 1509885 1510200 1510664 1512870 1518843 1528708 1556853 1573499 1574008 1583108 1599844 1601826 1605935 1623980 1624392 1624703 1674495 1674919 1675215 1683947 1684800 1702489 1702837 1728319 1731010 1737216 1745355 1751422 1755957 1757469 1781951 1782371 1783031 1789089 1799552 1799938 1801639 1812103 1865063 1866828 1882949 1900679 1918669 1931088 1933611 1936563 1946675 1955694 1977722 1999690 2002087 2006023 2051811 2060750 2087214 2096312 2100790 2123887 2124365 2129714 2147922 2165927 2184010 2201598 2210860 2229009 2235008 2236834 2246833 2254900 2264882 2287864 2288782 2293894 2339648 2357053 2358226 2557042 
15.0 11.047 9.218 2.158 5.651 1.582 2.557 9.021 1.705 0.53 4.516 3.345 6.886 2.406 3.403 1.492 9.277 17.808 11.794 12.835 0.849 1.079 1.731 2.322 3.498 11.344 3.557 2.855 5.115 4.854 3.743 2.121 13.609 7.568 1.211 3.205 2.682 13.918 14.59 0.463 8.497 1.495 0.796 3.21 1.725 1.491 2.618 3.747 0.6 4.053 2.03 1.492 1.949 1.192 1.328 10.994 13.943 4.254 3.338 2.735 3.014 5.191 10.215 5.438 5.624 5.791 3.259 1.786 2.164 2.535 16.179 2.477 1.535 2.042 1.796 5.098 6.093 2.313 0.112 14.538 2.319 9.645 1.996 3.562 2.684 1.298 1.014 17.673 1.767 1.412 4.747 2.337 1.795 2.516 1.277 12.698 0.952 1.283 3.906 1.704 6.473 6.453 1.343 5.453 11.15 4.047 4.544 5.806 7.674 16.82 5.754 0.628 2.577 3.213 2.799 2.795 5.316 4.358 4.657 6.45 1.673 2.75 1.816 1.634 0.618 1.822 4.59 10.042 6.122 2.589 1.216 11.894 1.768 16.089 19.967 2.792 2.214 5.295 3.614 7.599 14.916 3.696 0.165 2.278 2.66 6.027 7.18 3.713 2.3 5.614 1.426 2.467 0.457 5.003 0.456 0.827 5.153 5.097 8.034 7.42 3.365 0.042 4.159 0.331 0.405 0.518 0.574 2.061 0.126 1.605 5.348 3.205 0.658 2.201 6.024 4.347 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1250_0.prm:63
 Score: 129.225, AlignedPeaks: 0 200091 286841 445260 573224 674298 775266 872372 1056438 1155502 
0 198835 199521 200091 225963 262031 286841 356450 379187 409205 424087 427105 433303 438259 445260 451304 474035 486190 488202 520347 556315 557354 569229 573224 575296 587224 612269 622865 623291 670291 674298 731263 775266 775779 783209 793272 824451 832305 840207 872372 937268 955349 969537 973305 1008290 1008842 1026260 1031454 1045835 1056438 1121365 1125051 1137438 1155502 1218402 1236399 1254455 1286196 1318528 1320782 1329790 1367890 1368233 1368518 1381432 1392831 1399537 1411893 1415578 1418544 1480496 1491109 1528663 1563639 1567407 1581651 1599703 1635683 1663587 1664577 1668651 1696773 1704639 1712493 1725687 1743672 1753730 1761165 1761709 1779602 1797605 1826614 1862684 1913813 1914079 1924675 1961648 2109839 2127739 2157757 2180494 
15.0 1.923 1.469 2.1 6.581 2.069 1.768 2.744 3.625 3.745 5.762 5.552 4.523 3.31 12.073 1.437 5.58 5.203 3.616 8.201 4.594 5.401 5.126 9.452 1.621 0.028 1.056 3.574 8.09 1.026 12.995 1.903 27.471 8.755 5.247 3.009 2.35 1.852 3.641 6.79 19.183 9.154 0.26 0.001 17.795 1.734 0.039 1.031 0.535 8.286 2.064 0.212 2.838 18.29 16.193 2.733 1.077 2.899 17.885 3.196 2.461 1.651 0.437 2.798 16.057 1.992 5.53 0.543 1.231 1.624 6.484 0.825 18.934 1.475 0.698 3.544 20.287 0.04 2.329 3.292 0.292 7.053 1.268 0.567 1.447 0.378 6.842 21.447 19.363 2.372 1.865 2.181 1.681 3.432 1.367 2.446 1.623 2.687 0.947 1.17 1.922 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:752
 Score: 123.906, AlignedPeaks: 0 200275 287266 445186 573588 775297 872345 1056381 1155263 
0 127897 199271 200275 211902 228160 285480 287266 298234 392367 398774 409088 445186 464356 476072 479115 479918 512770 513500 515321 529299 559844 560317 561306 566850 573588 579383 655940 658648 677349 678022 680730 682349 685028 686381 756608 758925 761357 763183 767980 775297 776353 776826 781805 808547 817428 872345 891464 897157 909521 927662 937896 944303 957597 962455 986116 993268 994545 1006398 1035617 1049323 1056381 1108463 1155263 1155942 1187149 1190396 1318660 
15.0 0.792 8.186 22.234 0.711 6.105 0.481 5.103 5.939 0.911 0.467 5.083 11.364 5.559 0.759 2.088 1.832 3.543 3.872 2.411 0.491 2.83 3.352 12.151 3.086 6.162 1.621 0.456 0.201 3.025 3.913 0.35 0.119 1.594 4.389 0.598 2.898 1.249 5.986 5.445 13.225 6.855 7.337 1.0 1.294 2.265 6.334 4.817 0.855 2.692 5.617 0.871 0.151 0.525 1.048 0.004 0.699 0.991 2.018 0.655 4.594 17.758 2.408 11.726 4.48 1.271 4.341 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_925_0.prm:14
 Score: 114.227, AlignedPeaks: 0 200248 286929 445341 572929 674205 775391 872027 1056192 1155646 
0 174276 198654 200248 217962 253584 268095 275278 278469 286929 310198 320035 323356 338256 380350 394690 397396 409082 422052 424804 427157 444680 445341 463856 477498 510474 543388 565820 568911 572929 575146 587945 591534 601337 623281 623974 638465 650717 651406 668710 672290 674205 689536 708255 719463 728463 747842 757311 775391 809965 819141 846689 851491 852734 858646 862798 872027 876584 879697 885742 888308 903206 910728 913370 933226 968650 976320 1000160 1013664 1032435 1050684 1054437 1056192 1061892 1070398 1078813 1101131 1150837 1153656 1155646 1165241 1166033 1173139 1175208 1192126 1210839 1246487 1260793 1269847 1278604 1287461 1288258 1293687 1300447 1316757 1318565 1328788 1336449 1337122 1362585 1438048 1438721 1446382 1456529 1458413 1474723 1481483 1486912 1487709 1496566 1505323 1514377 1528683 1564331 1572496 1583044 1599905 1602031 1609137 1609929 1619545 1624333 1674039 1696357 1704772 1713278 1723730 1724486 1742735 1761506 1763537 1775010 1784029 1798850 1806520 1861800 1864442 1871964 1886862 1889428 1895473 1898586 1899290 1903143 1904968 1912372 1916524 1922436 1923679 1928481 1956029 1965205 1999779 2017859 2046707 2055706 2066915 2085634 2100965 2102880 2106460 2123764 2124453 2136705 2151196 2151889 2173833 2187225 2200024 2202257 2206259 2209350 2231782 2264696 2297672 2329829 2330484 2348013 2353118 2366088 2377774 2380480 2436914 2451814 2464972 2482699 2488241 2496701 2499892 2507075 2510727 2539694 2557208 2600894 2757160 
15.0 1.054 6.804 8.338 9.156 0.46 0.483 1.445 0.761 4.3 2.654 2.754 3.041 1.498 1.598 1.467 3.011 2.685 3.023 3.271 6.381 19.382 19.489 1.045 3.062 2.239 0.493 1.476 2.703 9.372 1.772 1.851 6.658 1.577 2.161 0.005 3.257 7.707 7.341 4.574 2.316 7.576 3.419 2.376 2.634 3.031 1.621 3.303 12.695 2.449 7.315 1.099 1.14 2.078 2.095 0.851 6.185 3.471 0.775 0.411 4.783 2.212 1.129 1.307 1.088 4.442 0.069 0.622 0.797 2.113 0.033 1.929 1.854 1.484 6.827 2.865 1.277 2.682 1.432 14.418 1.521 0.286 1.281 13.899 4.423 2.453 4.575 6.929 2.605 2.651 6.456 6.969 0.495 3.595 1.164 21.087 1.554 7.439 5.395 1.509 6.521 6.383 1.63 16.729 1.539 13.075 1.743 4.406 3.673 3.28 3.968 5.731 7.938 2.227 0.166 0.713 18.641 0.195 0.956 1.419 12.691 4.722 4.695 1.244 4.484 2.576 1.119 2.241 0.547 1.779 0.501 2.488 1.68 2.386 3.411 1.624 3.086 1.378 7.401 4.019 4.105 2.187 1.661 2.245 6.962 0.139 1.196 4.168 1.36 2.021 8.301 3.342 13.382 7.383 5.769 3.567 3.125 2.901 6.889 0.288 4.712 5.934 6.324 3.724 2.911 1.44 0.912 5.981 2.907 4.263 1.245 1.247 1.101 1.462 1.136 8.667 11.942 7.545 1.914 1.553 1.118 0.175 0.94 0.099 0.831 0.184 4.619 1.044 1.763 1.037 0.319 5.123 10.582 1.9 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:245
 Score: 110.81600000000002, AlignedPeaks: 0 200100 286735 445104 573244 674333 775303 872333 1056458 1155487 
0 199478 200100 201444 234022 266965 281178 286215 286735 287129 291887 292213 294480 298005 314169 316747 373142 389077 407004 426977 445104 460130 543370 557325 573244 575304 589223 670217 674333 674775 676245 688187 731285 775303 833268 851069 868218 870201 872333 876393 932265 955404 977128 979633 1012266 1024823 1031173 1031650 1033339 1040609 1056458 1094172 1116387 1120312 1137600 1155487 1188810 1197661 1213437 1266435 1278349 1313968 1314475 1318516 1393535 1399520 1413438 1415496 1423820 1445372 1500465 1510681 1528628 1543659 1599688 1615651 1674573 1696529 1702527 1707564 1708449 1753918 1754721 1970732 
15.0 5.567 5.937 1.813 4.042 0.344 2.494 7.315 6.122 5.199 0.859 0.825 1.303 5.648 1.946 3.19 7.694 19.32 7.486 0.502 10.587 19.835 0.494 1.882 7.238 1.163 0.726 14.998 6.007 0.856 0.086 0.511 0.182 17.289 14.469 9.136 3.737 1.287 7.022 0.782 7.113 0.945 0.918 0.58 2.805 0.872 5.833 5.325 0.367 2.707 4.98 3.538 3.075 3.485 5.779 15.634 2.556 2.09 13.177 1.255 1.462 6.135 8.087 15.046 1.309 0.766 7.717 7.51 1.643 0.005 1.01 1.867 20.538 5.798 27.342 2.437 2.067 0.189 0.778 0.801 0.558 8.076 8.456 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:247.5, InsertsAfter: 0
 * M[1] - Mass:199333.00000000003 Overlap:5/7 LogOddsScore:3.8326233110328936, SumScore:33.073, InsertsAfter: 3
 * M[2] - Mass:200091.39999999997 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:154.9485, InsertsAfter: 0
 * M[3] - Mass:286965.3333333334 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:78.942, InsertsAfter: 19
 * M[4] - Mass:298119.5 Overlap:2/7 LogOddsScore:0.08854268733673851, SumScore:11.587, InsertsAfter: 4
 * M[5] - Mass:373426.3333333333 Overlap:4/7 LogOddsScore:5.006081289134606, SumScore:48.7075, InsertsAfter: 11
 * M[6] - Mass:444699.0 Overlap:2/7 LogOddsScore:1.2992851136702874, SumScore:28.659, InsertsAfter: 22
 * M[7] - Mass:445251.6 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:331.69999999999993, InsertsAfter: 0
 * M[8] - Mass:573188.0666666668 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:395.871, InsertsAfter: 36
 * M[9] - Mass:674301.5833333335 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:391.75950000000006, InsertsAfter: 29
 * M[10] - Mass:775355.0666666668 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:527.856, InsertsAfter: 27
 * M[11] - Mass:872253.0666666667 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:357.5170000000001, InsertsAfter: 29
 * M[12] - Mass:1056323.8000000003 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:382.512, InsertsAfter: 65
 * M[13] - Mass:1155614.9999999998 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:456.05649999999997, InsertsAfter: 21
ConsensusPRM: 0 199333 200091 286965 298119 373426 444699 445251 573188 674301 775355 872253 1056323 1155614 Consensus: 0 199333 200091 286965 298119 373426 444699 445251 573188 674301 775355 872253 1056323 1155614
De Novo: [200.091]S[158.286]QTTP[184.07]V, Merged: [200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
0 199333 200091 286965 298119 373426 373988 444699 445251 573188 674301 775355 872253 1056323 1155614 1318746 1415860 1528944 1599981 1697033 1754054 1914138 1971159 2086185 2187232 2288279 2345300 2432332 2519364 2618432 2719479 2832563 2889584 3049668 3162752 3261820 3389914 3446935 3609998 3757066 3854118 3983160 4070192 4169260 4270307 4369375 4470422 4656501 4770543 4857575 4914596 5001628 5114712 5201744 5288776 5375808 5474876 5611934 5712981 5860049 5957101 6028138 6141222 6254306 6382364 6469396 6526417 6639501 6802564 6903611 7034651 7121683 7208715 7295747 7394815 7495862 7594930 7691982 7779014 7866046 7967093 8153172 8250224 8337256 8465314 8566361 8665429 8766476 8926560 9013592 9112660 9183697 9320755 9417807 9488844 9575876 9662908 9763955 9865002 9964070 10079096 10207190 10335284 10448368 10577410 10674462 10761494 10818515 10915567 11028651 11115683 11216730 11329814 11443856 11540908 11700992 11798044 11895096 12055180 12183274 12312316 12472400 12609458 12737552 12897636 12994688 13065725 13162777 13276819 13389903 13518945 13575966 13632987 13730039 13817071 13916139 14063207 14176291 14323359 14420411 14517463 14631505 14744589 14872683 14987709 15086777 15199861 15330901 15443985 15531017 15644101 15745148 15842200 15970294 16069362 16170409 16330493 
210.0 33.073 131.035 65.785 11.587 48.7075 34.1275 28.659 296.0395 374.087 371.66600000000005 485.221 343.04250000000013 363.35400000000004 421.5559999999999 317.20799999999997 273.612 270.0 270.0 270.0 270.0 255.0 255.0 300.0 300.0 270.0 330.0 315.0 330.0 285.0 300.0 345.0 330.0 390.0 510.0 540.0 585.0 360.0 405.0 405.0 405.0 645.0 690.0 765.0 1215.0 1200.0 1290.0 1515.0 1740.0 1710.0 1830.0 1845.0 1920.0 2025.0 1995.0 1965.0 1950.0 1995.0 1875.0 1770.0 1515.0 1515.0 1515.0 1200.0 945.0 480.0 480.0 435.0 450.0 255.0 240.0 225.0 195.0 240.0 240.0 240.0 225.0 225.0 225.0 225.0 225.0 225.0 225.0 195.0 195.0 150.0 120.0 180.0 330.0 345.0 330.0 360.0 360.0 375.0 375.0 375.0 390.0 390.0 375.0 375.0 450.0 1215.0 1320.0 1260.0 1365.0 1320.0 1350.0 1350.0 1350.0 1395.0 1410.0 1425.0 1335.0 1410.0 1260.0 1290.0 1290.0 1290.0 1290.0 1155.0 765.0 480.0 540.0 615.0 390.0 390.0 390.0 390.0 375.0 375.0 420.0 420.0 420.0 435.0 435.0 480.0 585.0 555.0 570.0 570.0 570.0 570.0 570.0 570.0 420.0 315.0 330.0 315.0 270.0 270.0 270.0 270.0 270.0 270.0 60.0 60.0 45.0 
(RIGHT)Round: 0 for seed: [200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_575_0.prm:6
 Score: 110.466, AlignedPeaks: 0 244120 331153 444230 545281 869501 1130572 
0 216125 244120 331153 444230 545281 565791 583295 593315 603302 639807 705362 722354 750349 817431 869501 904463 932466 1130572 
15.0 6.495 16.856 10.224 7.534 10.721 0.077 3.22 3.727 3.077 2.331 2.046 1.488 2.367 9.085 5.131 9.598 8.796 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:226
 Score: 108.43700000000001, AlignedPeaks: 0 112997 200021 312831 414059 639363 738309 839339 
0 112997 131005 200021 219965 312831 313456 321027 386058 386558 396771 414059 429825 431959 510133 514409 521660 538543 547572 552448 560399 588056 596977 629419 639363 645278 663167 672723 673223 680591 692057 738309 745825 746477 758098 764102 768945 776104 839339 928276 942368 1041271 
15.0 5.268 3.772 22.068 12.673 14.477 5.69 8.729 10.404 10.129 1.057 21.109 2.187 3.924 0.096 1.713 0.531 7.468 2.514 2.914 1.314 0.906 2.691 6.773 0.409 11.457 0.74 7.326 9.763 1.034 0.594 3.709 10.381 3.235 1.326 1.069 0.229 1.066 11.397 4.914 11.906 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_525_0.prm:200
 Score: 77.714, AlignedPeaks: 0 200113 313191 414244 738463 839509 
0 200113 220083 313191 321128 358662 414244 436759 588328 597337 629854 645348 692115 738463 764401 839509 942519 1041579 
15.0 13.498 7.441 10.064 8.199 0.937 15.296 0.426 1.185 2.035 1.151 4.568 1.358 3.219 4.554 5.637 5.991 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:345.0, InsertsAfter: 0
 * M[1] - Mass:131040.0 Overlap:4/5 LogOddsScore:8.621701717332472, SumScore:345.0, InsertsAfter: 1
 * M[2] - Mass:244087.6 Overlap:4/5 LogOddsScore:7.410959290998923, SumScore:292.12399999999997, InsertsAfter: 1
 * M[3] - Mass:331127.1428571428 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:315.78999999999996, InsertsAfter: 2
 * M[4] - Mass:444129.14285714284 Overlap:5/5 LogOddsScore:8.658986165564308, SumScore:302.075, InsertsAfter: 7
 * M[5] - Mass:545230.7142857143 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:317.126, InsertsAfter: 9
 * M[6] - Mass:642339.0 Overlap:2/5 LogOddsScore:3.704163115534604, SumScore:270.0, InsertsAfter: 15
 * M[7] - Mass:770413.0 Overlap:3/5 LogOddsScore:4.952189990099989, SumScore:270.409, InsertsAfter: 9
 * M[8] - Mass:869458.1428571428 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:72.059, InsertsAfter: 9
 * M[9] - Mass:970480.8 Overlap:4/5 LogOddsScore:6.200216864665374, SumScore:77.034, InsertsAfter: 3
 * M[10] - Mass:1130592.0 Overlap:3/5 LogOddsScore:5.6566571442724936, SumScore:60.0, InsertsAfter: 0
 * M[11] - Mass:1172465.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 0
ConsensusPRM: 0 131040 244087 331127 444129 545230 642339 770413 869458 970480 1130592 1172465 Consensus: 0 131040 244087 331127 444129 545230 642339 770413 869458 970480 1130592 1172465
De Novo: MISITPQVTC, Merged: [200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
0 200091 286965 373987 445251 573188 674301 775355 872253 1056323 1155613 1318745 1415859 1528943 1599980 1697032 1754053 1914137 1971158 2086184 2187231 2288278 2345299 2432331 2519363 2618431 2719478 2832562 2889583 3049667 3162751 3261819 3389913 3446934 3609997 3757065 3854117 3983159 4070191 4169259 4270306 4369374 4470421 4656500 4770542 4857574 4914595 5001627 5114711 5201743 5288775 5375807 5474875 5611933 5712980 5860048 5957100 6028137 6141221 6254305 6382363 6469395 6526416 6639500 6802563 6903610 7034650 7121682 7208714 7295746 7394814 7495861 7594929 7691981 7779013 7866045 7967092 8153171 8250223 8337255 8465313 8566360 8665428 8766475 8926559 9013591 9112659 9183696 9320754 9417806 9488843 9575875 9662907 9763954 9865001 9964069 10079095 10207189 10335283 10448367 10577409 10674461 10761493 10818514 10915566 11028650 11115682 11216729 11329813 11443855 11540907 11700991 11798043 11895095 12055179 12183273 12312315 12472399 12609457 12737551 12897635 12994687 13065724 13162776 13276818 13389902 13518944 13575965 13632986 13730038 13817070 13916138 14063206 14176290 14323358 14420410 14517462 14631504 14744588 14872682 14987708 15086776 15199860 15330900 15443984 15531016 15644100 15745147 15842199 15970293 16069361 16170408 16330492 16372365 
172.5 107.1215 52.628 34.1275 260.379 352.303 351.57250000000005 442.586 328.5680000000001 344.196 387.05549999999994 317.20799999999997 273.612 270.0 270.0 270.0 270.0 255.0 255.0 300.0 300.0 270.0 330.0 315.0 330.0 285.0 300.0 345.0 330.0 390.0 510.0 540.0 585.0 360.0 405.0 405.0 405.0 645.0 690.0 765.0 1215.0 1200.0 1290.0 1515.0 1740.0 1710.0 1830.0 1845.0 1920.0 2025.0 1995.0 1965.0 1950.0 1995.0 1875.0 1770.0 1515.0 1515.0 1515.0 1200.0 945.0 480.0 480.0 435.0 450.0 255.0 240.0 225.0 195.0 240.0 240.0 240.0 225.0 225.0 225.0 225.0 225.0 225.0 225.0 195.0 195.0 150.0 120.0 180.0 330.0 345.0 330.0 360.0 360.0 375.0 375.0 375.0 390.0 390.0 375.0 375.0 450.0 1215.0 1320.0 1260.0 1365.0 1320.0 1350.0 1350.0 1350.0 1395.0 1410.0 1425.0 1335.0 1410.0 1260.0 1290.0 1290.0 1290.0 1290.0 1155.0 765.0 480.0 540.0 615.0 390.0 390.0 390.0 390.0 375.0 375.0 420.0 420.0 420.0 435.0 435.0 480.0 585.0 555.0 570.0 570.0 570.0 570.0 570.0 570.0 420.0 315.0 337.5 328.3315668729493 279.39356687294924 292.895 286.0375 293.563 264.9947006188479 266.8676337458986 66.0295 66.8485668729493 49.16313374589859 30.0 

(LEFT)Round: 0 for seed: VVDVSEDDPDVQ
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:447
 Score: 80.72900000000001, AlignedPeaks: 1214850 1329512 1428516 1515537 1759758 1972192 
0 98895 113805 270192 270950 272893 282140 292731 293162 298226 309531 311131 322564 327182 345134 383215 386157 404172 415235 422337 457540 471535 472251 495015 499061 500112 515294 550071 550615 551420 607956 612127 621361 644340 655956 664761 665368 705183 714490 715431 725560 757940 785187 785807 814563 828367 830312 857561 901242 903912 907608 942526 943454 953875 959198 960404 998241 1043367 1046834 1063983 1065963 1068427 1083701 1089069 1103964 1128461 1129464 1130107 1131492 1167753 1186688 1187392 1194761 1214850 1224234 1232634 1236234 1240628 1242505 1258656 1260405 1296966 1306192 1311641 1322097 1327537 1329512 1330219 1331570 1346560 1347300 1410699 1411439 1426429 1428516 1430462 1435902 1446358 1451807 1461033 1497594 1499343 1515537 1517371 1525365 1533765 1563238 1570607 1571311 1590246 1626507 1628551 1629538 1654035 1654726 1668930 1674298 1689572 1692036 1694016 1711165 1714626 1754916 1759758 1797595 1798801 1804124 1814528 1815473 1850391 1854087 1856757 1900438 1927687 1929632 1943436 1944053 1952846 1972192 1972812 2000059 2032439 2042568 2043509 2052815 2092630 2093237 2102043 2113659 2136638 2145872 2150043 2193202 2206579 2207384 2242704 2257084 2257887 2285748 2286464 2300459 2309108 2335569 2342764 2353827 2371842 2374784 2412865 2435435 2446868 2464837 2465268 2475859 2479082 2485106 2487049 2487807 2612384 2739989 
15.0 5.237 2.715 4.085 2.847 2.04 0.534 9.732 10.032 0.907 2.37 5.103 3.38 0.178 2.527 1.75 2.161 4.036 2.35 9.68 0.53 1.541 2.537 1.137 3.218 1.471 1.259 1.153 7.21 7.592 1.73 3.653 5.885 1.438 2.336 7.554 2.412 1.192 2.041 2.476 2.895 1.522 1.828 1.471 2.573 2.049 6.875 3.181 3.283 3.452 5.076 16.849 19.323 2.635 4.002 5.079 2.441 9.936 0.731 2.314 0.687 2.665 1.759 1.49 2.556 4.691 13.853 11.505 0.446 1.009 6.235 7.448 1.646 1.916 4.7 1.279 1.55 1.493 20.986 0.957 0.244 2.256 6.897 4.903 2.169 4.641 28.504 13.9 4.375 0.735 9.305 2.565 3.145 6.122 24.486 3.488 1.926 11.956 5.779 1.926 0.456 0.783 20.347 0.524 2.356 11.134 1.614 7.274 3.985 3.285 2.84 18.096 3.803 1.038 6.176 0.574 1.697 1.243 1.554 3.102 5.376 9.035 0.937 2.082 4.479 4.104 1.763 22.053 20.327 7.712 3.509 2.925 2.915 7.951 0.536 3.97 2.98 4.392 3.394 3.264 4.676 3.042 3.381 5.83 2.759 7.06 11.105 3.905 4.717 9.097 1.146 2.363 6.434 5.69 6.391 2.872 0.334 2.666 1.431 1.2 0.592 0.531 8.83 5.093 0.154 1.358 0.202 2.603 0.414 2.181 9.055 9.055 0.372 1.336 1.773 3.354 1.951 5.521 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_525_0.prm:145
 Score: 78.114, AlignedPeaks: 980409 1079562 1293587 1380644 1624783 
0 154263 158153 168262 186100 214185 216314 281691 314971 318272 322562 349207 377178 386694 411718 417184 419766 423275 425614 476140 476650 494279 517126 535232 560448 563233 575301 593613 607473 623337 662311 668411 675297 676562 690322 694387 711457 736218 748521 773354 775479 790356 791438 807495 809433 818325 824469 835299 851284 852438 867315 869440 894273 906576 944032 948407 952472 962485 966232 974383 977519 980409 1009435 1067493 1068415 1079562 1111425 1112285 1125668 1148515 1152454 1166144 1166654 1217180 1219519 1223028 1225610 1231076 1256100 1265616 1281690 1293587 1311449 1320232 1327823 1330550 1336774 1361103 1380644 1397524 1399588 1426480 1428609 1456694 1497042 1624783 
15.0 0.227 1.153 0.548 2.409 1.881 1.288 0.222 1.907 3.162 0.343 1.164 7.725 1.243 0.921 1.85 3.504 0.938 0.123 6.696 6.664 6.042 9.887 0.079 0.714 11.335 1.762 0.9 0.771 1.072 22.03 0.446 0.496 1.672 6.388 1.831 1.207 0.916 0.669 3.932 0.751 0.856 21.631 4.683 1.974 0.816 0.453 1.332 20.25 1.914 1.232 5.612 1.136 0.781 1.586 0.368 2.632 1.781 2.72 0.696 0.077 24.497 0.163 1.284 0.094 22.043 0.544 0.009 6.159 1.571 2.803 3.786 13.443 0.847 0.502 5.266 1.06 0.837 1.703 12.825 1.599 1.308 2.379 0.762 1.672 0.33 7.342 2.239 0.266 0.202 1.568 1.495 0.27 2.882 7.325 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1275_0.prm:1
 Score: 74.675, AlignedPeaks: 401854 500914 715134 814293 900918 1030269 1145267 1260132 1357414 1472220 
0 215452 257882 301185 356984 358376 380010 392870 394354 401854 402989 415232 443281 467107 470340 480299 482815 483533 500914 501689 517104 534581 547164 581988 586206 597653 600525 613866 615713 669326 672935 682209 697124 699060 715134 735866 737799 746470 769229 780647 786432 796404 810900 814293 816558 818810 839254 873585 883336 900918 902370 906391 911802 912807 913594 943178 948391 994540 1012444 1013654 1028366 1029652 1030269 1095057 1096425 1116652 1145267 1186228 1200053 1205671 1233902 1237238 1240508 1245515 1260132 1265870 1302474 1321407 1339838 1357414 1372086 1393858 1394953 1418828 1447354 1455454 1469575 1472220 1496018 1506240 1510195 1542410 1546745 1547712 1615277 1642063 1664787 1675495 1680475 1708029 1718468 1719210 1736457 1737153 1762371 1765052 1786703 1790870 1862032 1886879 1889175 1890577 1892189 1895803 1907374 1920215 1923916 1935487 1939101 1940713 1942068 1944411 1969258 1981457 2040420 2044587 2066237 2068918 2094137 2094833 2112080 2112822 2123261 2150815 2155795 2166503 2189227 2216013 2283578 2284545 2288880 2321095 2325050 2335272 2359070 2361715 2375836 2383936 2412462 2436337 2437432 2459204 2473876 2491452 2509883 2528816 2565420 2571158 2585775 2590782 2594052 2597388 2625619 2631237 2645062 2686023 2714638 2734865 2736233 2801021 2801638 2802924 2817636 2818846 2836750 2882899 2888112 2917696 2918423 2924899 2928920 2930372 2947954 2957705 3016997 3034886 3044858 3050643 3062061 3116156 3132230 3134166 3149081 3161964 3215577 3217424 3230670 3245084 3249302 3296709 3314186 3327773 3329582 3330376 3347757 3348475 3364183 3388009 3416058 3428301 3429436 3436936 3438420 3451280 3472914 3474306 3524742 3530104 3573406 3581740 3657178 3685185 3813280 
15.0 3.694 2.211 3.335 2.515 2.885 1.427 1.69 1.862 2.224 1.576 5.055 4.664 0.547 2.315 2.664 4.541 4.28 16.176 14.393 0.016 2.008 3.437 2.604 2.575 2.265 12.795 1.682 2.572 4.746 2.172 2.058 1.583 4.093 7.091 2.19 5.411 1.65 3.77 2.065 5.904 2.715 3.065 10.303 1.446 6.528 2.888 2.283 4.846 5.631 2.69 2.184 2.665 2.577 2.536 2.837 2.706 7.899 6.406 2.843 3.148 5.245 8.548 7.448 6.813 8.142 3.936 3.413 7.581 2.773 1.137 4.866 3.268 1.944 4.259 2.146 1.864 6.427 6.683 13.149 1.643 2.852 2.173 0.946 7.907 1.393 0.01 3.358 1.242 1.823 1.768 1.491 2.034 2.93 2.9 4.826 3.081 3.004 3.023 3.609 2.512 0.456 7.105 4.264 1.774 2.173 0.778 3.664 0.801 3.389 3.879 5.925 3.929 0.664 1.203 0.528 0.765 2.977 1.341 4.3 2.969 4.316 0.896 0.792 6.791 4.204 3.528 2.334 2.724 3.776 2.248 3.048 5.21 2.679 3.487 4.168 5.356 1.642 2.876 4.002 0.977 3.67 5.947 3.142 4.911 1.551 1.992 3.433 3.128 5.416 7.435 3.735 7.002 10.201 7.439 4.858 2.319 6.236 2.316 3.361 5.079 1.212 2.068 9.204 2.604 5.58 6.077 4.241 5.983 6.914 5.676 3.938 3.588 5.156 3.512 2.947 2.618 4.455 4.101 3.456 4.342 4.196 4.236 2.166 9.334 3.372 1.652 0.54 0.525 9.544 4.917 1.581 1.037 3.045 1.159 1.117 13.0 1.174 3.15 0.143 0.19 1.049 5.535 11.088 1.863 1.598 1.083 3.54 0.962 0.791 1.005 0.309 0.005 1.681 2.531 2.389 2.237 3.274 1.867 5.842 0.465 2.182 15.0 

SpectrumHMM Model: * M[0] - Mass:-74017.0 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:21.532, InsertsAfter: 98
 * M[1] - Mass:0.0 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:32.224000000000004, InsertsAfter: 18
 * M[2] - Mass:99066.0 Overlap:4/5 LogOddsScore:8.115426445171428, SumScore:70.673, InsertsAfter: 25
 * M[3] - Mass:198253.5 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:66.754, InsertsAfter: 18
 * M[4] - Mass:313009.5 Overlap:4/5 LogOddsScore:7.157821654918401, SumScore:65.595, InsertsAfter: 26
 * M[5] - Mass:412127.5 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:66.09700000000001, InsertsAfter: 23
 * M[6] - Mass:499096.3333333333 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:56.244, InsertsAfter: 18
 * M[7] - Mass:628359.5 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:38.548, InsertsAfter: 28
 * M[8] - Mass:743285.8333333333 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:51.018, InsertsAfter: 13
 * M[9] - Mass:858317.0 Overlap:3/4 LogOddsScore:4.789844869623806, SumScore:34.259, InsertsAfter: 15
 * M[10] - Mass:955481.0 Overlap:4/4 LogOddsScore:7.24861417052274, SumScore:46.543, InsertsAfter: 10
 * M[11] - Mass:1070400.0 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:33.358, InsertsAfter: 13
ConsensusPRM: -74017 0 99066 198253 313009 412127 499096 628359 743285 858317 955481 1070400 Consensus: -74017 0 99066 198253 313009 412127 499096 628359 743285 858317 955481 1070400
De Novo: VVDVSEDDPD, Merged: VVDVSEDDPDVQ
-74017 0 99066 198253 313009 412127 499096 628359 743285 858317 955481 1070400 1169468 1297526 
21.532 31.112000000000002 50.3365 48.377 47.7975 48.048500000000004 43.122 34.274 40.509 32.1295 38.2715 31.679 30.0 30.0 
(RIGHT)Round: 0 for seed: VVDVSEDDPDVQ
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:7
 Score: 76.664, AlignedPeaks: 270851 386170 483183 598201 825491 
0 160173 183931 184547 199141 199849 202354 267967 270851 271781 289028 312246 327302 327977 342239 344978 369536 380268 384241 385548 386170 402111 404064 455073 457122 465176 483183 500776 511773 539450 553506 594222 596188 598201 598939 655209 708294 710054 714354 724077 726348 761817 821997 823242 825491 827282 843273 847506 867737 894215 941303 966122 983538 992205 993164 1008374 1055392 1057148 1066127 1066877 1075520 1110125 1126411 1138946 1147518 1149018 1166655 1167628 1175718 1176502 1223321 1239606 1241316 1250107 1294447 1331469 1332098 1350721 1351453 1353472 1355518 1396154 1398418 1400496 1410210 1437887 1452331 1466497 1492521 1494587 1510340 1563502 1564112 1621683 1622358 1678819 1681693 1747306 1768569 1789487 1931649 
15.0 0.719 11.078 6.896 0.256 0.136 3.582 1.611 10.525 3.929 7.619 3.76 10.004 12.733 1.169 7.411 3.876 0.542 6.46 18.005 32.367 7.236 14.056 0.454 9.588 0.865 16.354 1.373 0.542 0.638 0.234 5.735 0.021 14.986 1.464 6.686 13.557 1.903 4.092 0.22 15.081 0.463 5.184 6.782 2.432 5.76 1.197 1.597 2.937 4.745 7.144 0.892 2.83 6.647 2.238 5.019 6.859 7.496 5.887 4.818 2.943 6.713 9.3 2.539 2.423 1.018 2.002 8.687 2.13 10.94 6.626 1.132 15.229 6.778 6.414 4.366 3.057 0.62 8.46 0.615 5.638 0.401 0.819 0.527 0.419 1.24 1.268 11.28 5.859 1.68 1.391 33.051 7.198 7.442 11.262 10.084 1.495 1.812 3.347 0.781 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:168
 Score: 75.31, AlignedPeaks: 0 99020 186089 430292 757248 856266 984437 
0 99020 128207 146604 170220 184049 186089 202221 215178 257160 271104 285069 302091 314191 332287 343237 372146 384188 413159 430292 431286 455248 469316 471205 500249 504136 518370 542170 547231 554327 560141 572226 578322 599362 617290 634355 641250 687236 692248 695707 696225 701015 715330 727904 736784 740336 742495 751300 757248 802241 814382 827393 856266 885390 887253 901345 913352 926277 943414 968269 972381 984437 986440 1000432 1013292 1024281 1042366 1054518 1071516 1085488 1099448 1154324 1170480 1209965 1210296 1210663 1239610 1338558 
15.0 5.692 13.857 4.499 1.232 2.236 1.935 1.262 6.572 5.449 7.255 13.465 8.71 12.336 2.769 6.147 11.395 0.647 8.75 3.756 0.495 6.349 0.965 8.152 12.067 1.348 2.217 10.129 2.142 11.57 1.531 1.407 0.238 7.065 2.952 1.802 8.1 7.248 2.628 3.073 6.385 2.22 4.493 4.215 2.105 3.275 2.212 1.736 8.674 7.482 11.082 3.859 14.793 4.528 0.674 4.387 0.163 6.688 10.034 1.24 1.358 10.46 1.056 0.566 5.336 0.911 12.744 6.173 6.896 5.444 7.514 4.637 2.589 11.473 12.387 12.945 1.617 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_950_0.prm:45
 Score: 73.731, AlignedPeaks: 0 358916 456370 670322 
0 102859 128376 144030 213159 215037 232281 241279 259123 273144 275052 281309 283541 309135 311016 325011 326149 327264 342280 343214 344294 346676 354330 356153 358916 361101 413209 439076 440295 442210 455528 456370 458386 474041 493393 510147 524277 556239 557222 568984 569744 587435 593339 621350 652126 653250 670322 688380 690434 692417 771675 783385 784588 801483 804345 819516 884471 896522 975180 975787 980507 983358 984056 984820 989161 992279 992999 998421 1031740 1040256 1066361 1082327 1097452 1139945 1147725 1149539 1166554 1167797 1197641 1198569 1240568 1262655 1279735 1280859 1296649 1298049 1308796 1311635 1324746 1329709 1345550 1363241 1364001 1375821 1376746 1393853 1408708 1422838 1439623 1474599 1475678 1476588 1477457 1490787 1492690 1493909 1576832 1589771 1590830 1605721 1606836 1621969 1623850 1649444 1651676 1673862 1700704 1787028 1914975 
15.0 0.799 4.276 1.225 2.36 4.729 3.754 8.046 4.741 0.211 1.081 0.431 1.064 0.033 2.647 0.795 2.801 10.975 9.787 9.015 8.182 5.966 4.377 0.613 5.171 6.615 3.186 0.344 1.522 6.088 3.345 15.581 3.133 4.412 5.166 0.423 0.042 5.308 13.049 1.746 2.679 2.33 2.807 0.991 0.375 2.593 22.979 4.212 1.478 1.798 5.418 20.253 6.337 7.563 2.837 1.873 7.892 3.813 2.876 1.285 1.007 6.618 8.078 3.183 2.721 3.166 1.339 2.5 3.708 3.409 4.34 3.335 2.977 1.399 2.327 13.12 8.742 1.593 6.048 2.429 0.312 13.15 7.039 2.178 0.673 5.867 1.147 1.563 0.917 0.074 0.507 2.039 1.607 11.865 3.391 0.967 1.469 2.999 3.633 1.437 3.256 13.714 5.344 5.033 2.447 1.741 0.406 16.401 12.154 2.205 1.459 0.187 1.153 0.053 0.75 4.985 2.366 3.278 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:61
 Score: 71.387, AlignedPeaks: 358156 685145 800275 899378 
0 238841 241022 256973 260391 261019 278123 323097 341013 341790 342344 349247 355155 358156 373144 374099 376076 388294 392123 393950 429116 451208 460317 469149 486072 508181 521236 537192 539212 541048 543128 556184 557310 614210 658240 658677 668293 683125 684228 685145 685872 686221 701316 782302 782786 800275 800930 883265 896321 899378 912427 914283 958872 968358 1000292 1002349 1009399 1013073 1053463 1088274 1096236 1096968 1145719 1149401 1156417 1158500 1199920 1246365 1259418 1262454 1277427 1351715 1358518 1371164 1376006 1376520 1393456 1393733 1394231 1457477 1472921 1473647 1481350 1490521 1492467 1500489 1544587 1559730 1561559 1579560 1602609 1615665 1632610 1637560 1650611 1672786 1729676 1782717 1784694 1800659 1816480 1816985 1880669 1897774 1898401 1901819 1966360 2140782 
15.0 0.722 7.331 0.715 1.731 3.521 0.743 0.587 8.048 12.409 11.96 0.122 1.58 23.304 4.172 7.255 21.249 2.361 8.618 4.614 4.562 2.212 1.84 3.01 11.969 0.213 9.485 3.27 6.451 1.202 1.618 1.83 1.067 18.823 3.062 2.68 11.129 0.166 0.23 6.513 2.449 2.449 14.637 5.753 5.052 21.457 4.256 1.113 8.682 20.113 1.683 3.58 0.036 3.472 0.412 13.088 3.433 0.343 0.789 7.328 3.935 7.871 1.719 13.021 4.634 0.837 0.15 0.114 4.03 16.583 1.326 0.535 4.833 0.568 22.432 23.251 6.116 2.982 0.661 1.722 1.958 0.037 0.5 13.558 2.917 4.592 5.737 1.56 7.428 1.173 0.194 0.892 2.444 16.533 0.41 6.492 0.253 6.913 1.745 28.215 5.832 6.602 1.915 2.328 1.795 0.314 1.127 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:30.0, InsertsAfter: 0
 * M[1] - Mass:115026.0 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
 * M[2] - Mass:214058.0 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:35.692, InsertsAfter: 5
 * M[3] - Mass:301120.5 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:46.935, InsertsAfter: 7
 * M[4] - Mass:429470.5 Overlap:2/5 LogOddsScore:0.7764029907064618, SumScore:16.612000000000002, InsertsAfter: 3
 * M[5] - Mass:458268.5 Overlap:2/5 LogOddsScore:0.7764029907064618, SumScore:17.225, InsertsAfter: 12
 * M[6] - Mass:545247.1428571428 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:44.281, InsertsAfter: 35
 * M[7] - Mass:660307.1666666666 Overlap:4/5 LogOddsScore:7.157821654918401, SumScore:67.538, InsertsAfter: 19
 * M[8] - Mass:757074.4444444445 Overlap:5/5 LogOddsScore:9.363453319736813, SumScore:70.035, InsertsAfter: 26
 * M[9] - Mass:872393.142857143 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:53.660000000000004, InsertsAfter: 10
 * M[10] - Mass:971356.3333333334 Overlap:4/5 LogOddsScore:8.115426445171428, SumScore:67.77199999999999, InsertsAfter: 22
 * M[11] - Mass:1099616.4285714286 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:42.892, InsertsAfter: 61
 * M[12] - Mass:1450755.0 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:24.06, InsertsAfter: 75
ConsensusPRM: 0 115026 214058 301120 429470 458268 545247 660307 757074 872393 971356 1099616 1450755 Consensus: 0 115026 214058 301120 429470 458268 545247 660307 757074 872393 971356 1099616 1450755
De Novo: DVS[244.127]DPDVK[351.139], Merged: VVDVSEDDPDVQ[351.139]
0 99068 198136 313162 412230 499262 627414 628304 656212 743330 858356 955408 1070434 1169502 1297560 1648699 
30.0 30.0 30.0 37.5 32.846000000000004 36.7990668729493 6.601401237695772 30.0 7.214401237695771 35.4720668729493 47.100566872949294 50.0175 40.161566872949294 47.21756687294929 34.77756687294929 20.72313374589859 
(RIGHT)Round: 1 for seed: VVDVSEDDPDVQ[351.139]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_975_0.prm:7
 Score: 87.604, AlignedPeaks: 270851 386170 483183 598201 825491 1176502 
0 160173 183931 184547 199141 199849 202354 267967 270851 271781 289028 312246 327302 327977 342239 344978 369536 380268 384241 385548 386170 402111 404064 455073 457122 465176 483183 500776 511773 539450 553506 594222 596188 598201 598939 655209 708294 710054 714354 724077 726348 761817 821997 823242 825491 827282 843273 847506 867737 894215 941303 966122 983538 992205 993164 1008374 1055392 1057148 1066127 1066877 1075520 1110125 1126411 1138946 1147518 1149018 1166655 1167628 1175718 1176502 1223321 1239606 1241316 1250107 1294447 1331469 1332098 1350721 1351453 1353472 1355518 1396154 1398418 1400496 1410210 1437887 1452331 1466497 1492521 1494587 1510340 1563502 1564112 1621683 1622358 1678819 1681693 1747306 1768569 1789487 1931649 
15.0 0.719 11.078 6.896 0.256 0.136 3.582 1.611 10.525 3.929 7.619 3.76 10.004 12.733 1.169 7.411 3.876 0.542 6.46 18.005 32.367 7.236 14.056 0.454 9.588 0.865 16.354 1.373 0.542 0.638 0.234 5.735 0.021 14.986 1.464 6.686 13.557 1.903 4.092 0.22 15.081 0.463 5.184 6.782 2.432 5.76 1.197 1.597 2.937 4.745 7.144 0.892 2.83 6.647 2.238 5.019 6.859 7.496 5.887 4.818 2.943 6.713 9.3 2.539 2.423 1.018 2.002 8.687 2.13 10.94 6.626 1.132 15.229 6.778 6.414 4.366 3.057 0.62 8.46 0.615 5.638 0.401 0.819 0.527 0.419 1.24 1.268 11.28 5.859 1.68 1.391 33.051 7.198 7.442 11.262 10.084 1.495 1.812 3.347 0.781 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_950_0.prm:45
 Score: 86.851, AlignedPeaks: 0 358916 456370 670322 1149539 
0 102859 128376 144030 213159 215037 232281 241279 259123 273144 275052 281309 283541 309135 311016 325011 326149 327264 342280 343214 344294 346676 354330 356153 358916 361101 413209 439076 440295 442210 455528 456370 458386 474041 493393 510147 524277 556239 557222 568984 569744 587435 593339 621350 652126 653250 670322 688380 690434 692417 771675 783385 784588 801483 804345 819516 884471 896522 975180 975787 980507 983358 984056 984820 989161 992279 992999 998421 1031740 1040256 1066361 1082327 1097452 1139945 1147725 1149539 1166554 1167797 1197641 1198569 1240568 1262655 1279735 1280859 1296649 1298049 1308796 1311635 1324746 1329709 1345550 1363241 1364001 1375821 1376746 1393853 1408708 1422838 1439623 1474599 1475678 1476588 1477457 1490787 1492690 1493909 1576832 1589771 1590830 1605721 1606836 1621969 1623850 1649444 1651676 1673862 1700704 1787028 1914975 
15.0 0.799 4.276 1.225 2.36 4.729 3.754 8.046 4.741 0.211 1.081 0.431 1.064 0.033 2.647 0.795 2.801 10.975 9.787 9.015 8.182 5.966 4.377 0.613 5.171 6.615 3.186 0.344 1.522 6.088 3.345 15.581 3.133 4.412 5.166 0.423 0.042 5.308 13.049 1.746 2.679 2.33 2.807 0.991 0.375 2.593 22.979 4.212 1.478 1.798 5.418 20.253 6.337 7.563 2.837 1.873 7.892 3.813 2.876 1.285 1.007 6.618 8.078 3.183 2.721 3.166 1.339 2.5 3.708 3.409 4.34 3.335 2.977 1.399 2.327 13.12 8.742 1.593 6.048 2.429 0.312 13.15 7.039 2.178 0.673 5.867 1.147 1.563 0.917 0.074 0.507 2.039 1.607 11.865 3.391 0.967 1.469 2.999 3.633 1.437 3.256 13.714 5.344 5.033 2.447 1.741 0.406 16.401 12.154 2.205 1.459 0.187 1.153 0.053 0.75 4.985 2.366 3.278 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:168
 Score: 75.31, AlignedPeaks: 0 99020 186089 430292 757248 856266 984437 
0 99020 128207 146604 170220 184049 186089 202221 215178 257160 271104 285069 302091 314191 332287 343237 372146 384188 413159 430292 431286 455248 469316 471205 500249 504136 518370 542170 547231 554327 560141 572226 578322 599362 617290 634355 641250 687236 692248 695707 696225 701015 715330 727904 736784 740336 742495 751300 757248 802241 814382 827393 856266 885390 887253 901345 913352 926277 943414 968269 972381 984437 986440 1000432 1013292 1024281 1042366 1054518 1071516 1085488 1099448 1154324 1170480 1209965 1210296 1210663 1239610 1338558 
15.0 5.692 13.857 4.499 1.232 2.236 1.935 1.262 6.572 5.449 7.255 13.465 8.71 12.336 2.769 6.147 11.395 0.647 8.75 3.756 0.495 6.349 0.965 8.152 12.067 1.348 2.217 10.129 2.142 11.57 1.531 1.407 0.238 7.065 2.952 1.802 8.1 7.248 2.628 3.073 6.385 2.22 4.493 4.215 2.105 3.275 2.212 1.736 8.674 7.482 11.082 3.859 14.793 4.528 0.674 4.387 0.163 6.688 10.034 1.24 1.358 10.46 1.056 0.566 5.336 0.911 12.744 6.173 6.896 5.444 7.514 4.637 2.589 11.473 12.387 12.945 1.617 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:52.5, InsertsAfter: 0
 * M[1] - Mass:99036.0 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:38.538000000000004, InsertsAfter: 5
 * M[2] - Mass:186096.33333333334 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:53.7340668729493, InsertsAfter: 7
 * M[3] - Mass:314492.0 Overlap:2/5 LogOddsScore:0.7764029907064618, SumScore:16.612000000000002, InsertsAfter: 3
 * M[4] - Mass:343242.5 Overlap:2/5 LogOddsScore:0.7764029907064618, SumScore:17.225, InsertsAfter: 12
 * M[5] - Mass:430209.3333333333 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:49.7530668729493, InsertsAfter: 35
 * M[6] - Mass:545243.2857142858 Overlap:4/5 LogOddsScore:7.157821654918401, SumScore:84.6385668729493, InsertsAfter: 19
 * M[7] - Mass:642184.0 Overlap:5/5 LogOddsScore:9.363453319736813, SumScore:90.0525, InsertsAfter: 26
 * M[8] - Mass:757386.9999999999 Overlap:4/5 LogOddsScore:6.904684018837878, SumScore:63.8215668729493, InsertsAfter: 10
 * M[9] - Mass:856356.3333333334 Overlap:4/5 LogOddsScore:8.115426445171428, SumScore:84.9895668729493, InsertsAfter: 22
 * M[10] - Mass:984616.0 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:47.6695668729493, InsertsAfter: 61
 * M[11] - Mass:1335701.5714285714 Overlap:4/5 LogOddsScore:4.483199166170781, SumScore:44.78313374589859, InsertsAfter: 40
 * M[12] - Mass:1625768.5 Overlap:2/2 LogOddsScore:1.808193445761047, SumScore:14.913, InsertsAfter: 33
ConsensusPRM: 0 99036 186096 314492 343242 430209 545243 642184 757386 856356 984616 1335701 1625768 Consensus: 0 99036 186096 314492 343242 430209 545243 642184 757386 856356 984616 1335701 1625768
De Novo: VS[244.113]DPDVK[351.085], Merged: VVDVSEDDPDVQ[351.139]
0 99068 198136 313162 412230 499262 627490 628304 656240 743330 858356 955408 1070434 1169502 1297560 1648699 1938766 
30.0 30.0 30.0 45.0 35.69200000000001 43.59813374589859 6.601401237695772 30.0 7.214401237695771 40.9441337458986 64.20113374589859 70.035 50.32313374589859 64.43513374589858 39.55513374589859 31.084700618847883 14.913 

(LEFT)Round: 0 for seed: FVNNVEVHTAQTQTHRE
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:259
 Score: 77.988, AlignedPeaks: 1064376 1163392 1277361 1391479 
0 183763 260098 261576 267417 278904 283930 286104 296130 297463 299063 324173 375252 389281 393225 409328 410835 417098 446225 463544 472057 524516 533214 550063 560198 567566 603227 619128 621180 647322 664852 682410 706209 761284 777297 779281 790148 807287 819668 860321 864257 876987 878418 895581 916251 937120 970710 971320 980064 987580 989368 1008449 1064376 1081435 1095586 1105032 1134552 1147403 1152431 1163392 1170753 1180345 1218495 1235618 1277361 1294488 1321467 1338682 1356544 1357134 1364502 1366657 1391479 1452643 1461156 1478494 1507597 1524705 1549490 1566483 1627237 1638596 1645796 1663124 1664602 1743383 1759426 1762896 1778591 1906689 
15.0 1.68 3.111 4.417 8.141 2.279 2.357 6.834 4.609 3.901 0.967 3.664 6.44 1.277 7.353 2.765 2.014 19.094 4.888 2.762 0.738 0.317 2.395 2.967 0.186 1.907 23.104 0.796 2.091 7.762 0.544 0.932 16.358 5.699 3.844 4.578 1.042 9.682 0.247 6.116 8.751 2.141 2.564 6.461 0.172 0.13 7.773 10.021 6.306 1.734 0.553 2.078 20.631 0.12 3.475 0.853 0.319 0.044 0.102 23.136 3.259 2.42 2.019 3.625 19.817 0.147 3.844 10.479 0.934 1.005 2.442 1.712 14.404 1.044 0.572 11.161 12.719 5.829 15.028 0.026 0.207 1.584 0.856 4.77 2.994 2.2 1.177 1.505 11.81 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_425_0.prm:459
 Score: 75.011, AlignedPeaks: 386189 533262 632329 860407 
0 246091 345159 350115 350617 359175 373147 386189 403213 447720 448211 492231 519241 533262 550279 632329 860407 
15.0 15.122 12.2 3.557 1.91 2.939 2.103 16.219 2.504 0.915 3.973 5.873 0.108 12.363 1.23 16.429 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:46.219, InsertsAfter: 7
 * M[1] - Mass:147070.5 Overlap:3/3 LogOddsScore:5.640050293469712, SumScore:72.363, InsertsAfter: 5
 * M[2] - Mass:246138.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:76.429, InsertsAfter: 1
 * M[3] - Mass:360178.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:60.0, InsertsAfter: 0
 * M[4] - Mass:474219.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:75.0, InsertsAfter: 0
 * M[5] - Mass:573288.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:60.0, InsertsAfter: 0
 * M[6] - Mass:702330.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:135.0, InsertsAfter: 0
 * M[7] - Mass:801398.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:135.0, InsertsAfter: 0
 * M[8] - Mass:938456.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:135.0, InsertsAfter: 0
 * M[9] - Mass:1039503.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:105.0, InsertsAfter: 0
 * M[10] - Mass:1110540.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:75.0, InsertsAfter: 0
ConsensusPRM: 0 147070 246138 360178 474219 573288 702330 801398 938456 1039503 1110540 Consensus: 0 147070 246138 360178 474219 573288 702330 801398 938456 1039503 1110540
De Novo: FVNNVEVHTA, Merged: FVNNVEVHTAQTQTHRE
0 147070 246138 360178 474219 573288 702330 801398 938456 1039503 1110540 1238598 1339645 1467703 1568750 1705808 1861909 1990951 
38.1095 66.1815 68.2145 60.0 67.5 60.0 135.0 135.0 135.0 105.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 
(RIGHT)Round: 0 for seed: FVNNVEVHTAQTQTHRE
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_625_0.prm:226
 Score: 77.769, AlignedPeaks: 241848 370161 700222 1122733 
0 241169 241848 258779 294305 308576 369142 370161 407315 443343 451255 454395 494842 500222 504742 518364 527223 537913 580678 587428 588669 633893 679439 684838 693263 693755 699240 700222 702378 717392 718564 764721 769616 783521 814227 816146 821343 830296 838607 886563 888829 908437 925510 927420 928494 942434 945600 994564 1008504 1009511 1011488 1028542 1033596 1048169 1050435 1089409 1097889 1098391 1106702 1115584 1122733 1123884 1153477 1167382 1190018 1198866 1218434 1219606 1234620 1236759 1237758 1243243 1243735 1252160 1303105 1318571 1326657 1327057 1327312 1348329 1349570 1356320 1371830 1375556 1384131 1384703 1389600 1399085 1409775 1418634 1432256 1436776 1441087 1482603 1485743 1493655 1529647 1538344 1546910 1566956 1567856 1582833 1584880 1586680 1640785 1642639 1678218 1679816 1695171 1703763 1722744 1918988 
15.0 16.704 27.338 0.457 6.043 1.618 8.357 8.66 7.103 7.388 1.484 0.617 0.414 7.705 0.175 0.993 0.87 0.8 2.764 4.822 3.176 0.057 0.632 2.416 4.164 4.304 4.33 16.226 1.216 6.266 10.43 1.168 1.55 1.267 18.617 0.076 5.334 2.133 5.599 0.8 0.788 8.016 8.889 19.399 2.047 1.458 6.642 0.088 0.24 21.696 6.962 14.62 3.289 1.563 3.765 1.035 0.04 4.053 0.351 6.354 25.545 0.826 1.514 0.147 1.368 2.938 7.474 1.08 0.315 24.774 2.44 5.303 5.571 1.055 1.657 0.313 0.852 0.527 0.851 4.423 3.194 1.017 2.87 0.858 0.667 0.51 0.414 0.224 0.018 4.745 0.489 6.894 0.903 3.974 1.724 10.184 11.163 0.626 1.41 9.996 5.859 1.705 0.644 3.323 1.093 6.194 2.689 1.615 10.661 2.383 3.265 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1175_0.prm:57
 Score: 74.625, AlignedPeaks: 0 329801 623098 752073 
0 329801 339459 356417 368194 393168 396225 406804 409177 412360 426643 429247 439087 447091 455966 457159 458950 473868 477671 498240 510389 514405 524837 526172 526850 527454 528322 557582 623098 639152 643442 672319 684346 704354 737999 752073 769086 787174 791419 795532 799360 808306 822889 823320 825501 833566 865735 887951 912484 928963 932552 933258 939469 950686 971322 979104 993420 1011439 1028449 1028935 1033148 1034281 1116751 1120638 1121289 1121875 1140387 1146875 1204473 1205249 1228047 1234424 1242957 1252949 1253551 1340477 1345889 1346375 1352173 1361202 1363342 1366280 1424138 1439081 1445861 1462325 1509089 1549323 1551504 1551935 1566518 1575430 1583405 1605738 1622759 1634590 1636825 1670470 1690499 1725978 1731382 1735672 1751761 1788328 1789546 1790621 1817242 1818812 1846532 1848652 1917651 1918858 1935737 1945577 1962464 1978599 2006630 2018407 2035365 2045023 2356814 
15.0 6.488 2.913 5.272 3.997 5.403 6.841 4.202 0.478 1.327 3.534 6.657 0.011 3.187 7.011 16.866 2.476 6.076 3.446 2.368 4.582 5.231 3.695 9.788 4.618 4.666 9.874 0.826 22.605 1.903 0.504 0.61 9.97 0.227 1.036 15.532 0.276 0.37 0.057 0.636 9.53 0.644 5.273 5.706 0.194 0.445 2.489 0.123 8.926 1.119 0.756 1.719 1.292 0.179 1.208 3.363 0.128 13.813 5.314 5.45 4.677 11.162 0.677 7.945 13.948 2.395 8.279 6.071 0.853 2.066 2.336 7.483 1.158 6.777 13.101 10.678 8.164 8.46 3.594 1.171 16.547 0.062 1.303 0.483 0.792 10.047 0.055 0.876 3.351 3.302 0.769 12.07 2.173 1.005 9.179 1.085 1.121 0.492 11.456 1.416 1.353 3.183 20.95 1.557 2.462 1.163 1.625 0.779 5.409 11.783 11.188 1.11 1.469 5.606 0.942 1.39 1.144 3.002 1.032 6.55 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:212
 Score: 74.03, AlignedPeaks: 0 229130 356992 458286 595501 
0 114542 130991 225196 227981 229130 240735 241344 243564 247298 260161 300110 324054 328339 331225 339235 341987 343371 356106 356992 357604 359004 361349 373217 373994 375147 395595 402225 443483 457384 458286 459714 466598 475384 484986 496442 515347 517198 526392 541114 549263 572317 594504 595501 625112 630760 632264 643249 659135 662210 671447 673424 680021 686308 687697 708587 758387 759125 770221 790365 804879 810820 818065 835930 855271 864320 872306 898335 899097 905305 905966 977077 1012735 1013343 1016867 1020388 1025356 1025968 1030954 1034699 1039473 1043290 1073976 1082730 1089845 1128250 1148453 1152596 1156353 1160314 1165454 1210114 1231004 1232393 1238680 1245277 1247254 1249663 1256491 1259566 1263800 1275425 1287941 1297924 1324197 1330193 1341498 1346313 1350475 1369438 1377587 1381679 1392309 1403354 1433715 1437959 1443317 1448027 1452103 1460369 1461317 1475218 1543554 1561097 1561719 1562595 1575330 1576714 1618589 1671403 1675137 1683530 1689571 1690720 1785503 1786434 1787083 1787709 1900691 
15.0 12.006 1.809 2.518 3.088 14.827 2.881 2.044 2.817 5.238 4.65 4.524 2.909 1.59 0.953 0.628 5.541 3.657 4.675 14.433 10.569 6.451 4.132 4.165 0.403 6.893 0.537 2.698 3.296 8.291 13.86 2.185 1.244 0.99 0.774 0.496 0.966 0.864 0.497 0.151 0.492 13.192 1.409 0.91 1.63 0.705 1.961 12.012 0.173 0.879 0.994 1.405 1.171 1.255 1.26 1.616 1.527 2.203 13.972 5.593 3.014 2.502 2.371 4.634 4.399 2.977 2.75 8.354 2.555 8.828 5.642 3.15 4.423 3.455 10.044 7.762 5.673 6.118 4.053 2.563 3.285 1.83 3.387 6.146 3.464 10.396 6.092 1.832 2.82 0.363 2.714 0.395 2.41 2.645 0.596 0.233 0.269 1.284 2.902 2.148 4.45 14.132 0.126 0.875 1.098 1.239 0.408 9.642 0.4 0.909 2.473 1.207 1.245 0.722 1.316 1.27 1.109 1.813 1.417 10.03 8.44 0.606 1.909 9.948 10.512 0.024 4.392 1.185 3.581 3.834 5.822 0.612 20.742 7.158 6.28 7.385 4.655 2.07 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_725_0.prm:436
 Score: 73.92399999999999, AlignedPeaks: 315057 443314 544261 837274 
0 156443 174122 186008 204348 314028 315057 344246 387427 443314 461200 490261 508373 544261 585364 621893 628262 628709 632878 642338 651123 659292 744130 746253 752870 753245 774730 796798 797277 811327 828306 837274 837766 885280 886714 892207 892943 901307 901707 902054 926381 964279 970310 980414 983331 1005401 1027333 1044785 1047305 1083252 1087455 1100567 1126395 1136269 1137753 1155580 1156616 1183481 1197509 1246466 1262213 1266296 1278584 1284636 1296522 1452634 
15.0 1.489 7.109 10.373 3.911 3.504 33.783 2.936 3.852 21.151 3.093 1.954 0.132 10.125 0.148 0.517 2.157 2.869 4.622 0.614 2.611 14.485 10.406 2.524 1.557 2.697 0.588 1.115 1.724 6.784 0.662 8.865 7.697 0.779 2.556 2.208 12.06 0.327 0.844 1.752 7.036 0.418 1.74 8.135 1.469 0.02 1.207 1.446 1.048 7.013 0.395 1.439 6.145 1.335 1.061 23.133 4.013 1.662 1.138 0.078 0.793 3.185 1.732 11.477 12.06 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:135.0, InsertsAfter: 0
 * M[1] - Mass:137058.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:135.0, InsertsAfter: 0
 * M[2] - Mass:238105.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:105.0, InsertsAfter: 0
 * M[3] - Mass:309142.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:90.0, InsertsAfter: 1
 * M[4] - Mass:437200.0 Overlap:3/4 LogOddsScore:6.506862568118399, SumScore:90.0, InsertsAfter: 3
 * M[5] - Mass:538263.6666666667 Overlap:3/4 LogOddsScore:6.506862568118399, SumScore:89.827, InsertsAfter: 13
 * M[6] - Mass:666191.0 Overlap:3/4 LogOddsScore:6.506862568118399, SumScore:89.43299999999999, InsertsAfter: 10
 * M[7] - Mass:767242.0 Overlap:4/4 LogOddsScore:7.754889442683784, SumScore:95.348, InsertsAfter: 27
 * M[8] - Mass:904565.3333333333 Overlap:3/4 LogOddsScore:5.296120141784851, SumScore:75.91, InsertsAfter: 23
 * M[9] - Mass:1060369.0 Overlap:3/4 LogOddsScore:6.506862568118399, SumScore:97.605, InsertsAfter: 17
 * M[10] - Mass:1189366.3333333333 Overlap:3/4 LogOddsScore:6.506862568118399, SumScore:90.532, InsertsAfter: 58
 * M[11] - Mass:1558647.0 Overlap:2/2 LogOddsScore:3.0189358720945956, SumScore:15.232000000000001, InsertsAfter: 97
ConsensusPRM: 0 137058 238105 309142 437200 538263 666191 767242 904565 1060369 1189366 1558647 Consensus: 0 137058 238105 309142 437200 538263 666191 767242 904565 1060369 1189366 1558647
De Novo: HTAQTQTHRE, Merged: FVNNVEVHTAQTQTHRE
0 147068 246136 360178 474220 573288 702330 801398 938456 1039503 1110540 1238598 1339645 1467703 1568750 1705808 1861909 1990951 2360232 
30.0 60.0 60.0 60.0 60.0 60.0 135.0 135.0 135.0 105.0 82.5 80.8315668729493 80.7450668729493 80.54806687294929 85.174 73.7865668729493 84.63406687294929 81.0975668729493 15.232000000000001 

(LEFT)Round: 0 for seed: RVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSL
(RIGHT)Round: 0 for seed: RVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSL
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_475_0.prm:205
 Score: 88.163, AlignedPeaks: 0 99062 186148 299151 
0 99062 186148 299151 316166 317150 323172 360612 427180 451259 485411 505065 514510 519582 542137 546185 566230 589478 597592 598325 646113 670239 694239 771326 807254 828267 975392 
15.0 10.366 24.516 23.281 10.339 1.917 6.015 0.828 8.594 6.633 1.336 2.74 1.934 1.465 6.399 1.333 1.935 5.786 0.533 0.735 1.7 7.66 7.882 9.084 18.7 11.193 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_600_0.prm:566
 Score: 81.375, AlignedPeaks: 491357 578368 977340 1163508 1276599 
0 146602 171822 186208 204310 244140 244963 245628 336800 355044 355931 357130 382577 392037 429318 431251 431522 449351 488648 491357 511363 556711 558788 559375 560282 578368 578967 594252 598097 603633 640091 640580 671328 672814 673359 689439 691524 707615 790706 795992 796374 814196 823586 857637 859437 877650 895199 895601 895933 959238 977340 991438 1004355 1022577 1040513 1040896 1109255 1109732 1129273 1145364 1147449 1163508 1164074 1196797 1198695 1236473 1238791 1242636 1255083 1258341 1276599 1277513 1280177 1313797 1325525 1343796 1345531 1348239 1357287 1387537 1405366 1405636 1407045 1444851 1472742 1479758 1480957 1481844 1500088 1554892 1565626 1591260 1591970 1594779 1607857 1632578 1650680 1655477 1665067 1690286 1690900 1818877 
15.0 3.602 5.382 0.113 0.668 0.133 9.413 9.374 2.181 1.749 1.579 0.731 1.569 8.681 0.192 15.323 17.874 0.925 4.203 1.952 1.023 3.506 0.457 0.874 15.406 6.094 1.981 0.548 0.266 0.82 7.966 7.388 0.515 8.218 18.216 0.698 4.285 2.595 3.143 1.514 1.417 12.504 0.123 0.761 22.27 11.669 1.603 1.603 0.576 2.8 29.748 0.902 0.534 9.294 4.377 0.675 1.164 2.4 4.261 1.67 0.727 24.353 11.749 8.164 0.165 0.358 0.256 0.031 0.376 0.682 19.228 0.364 0.62 0.596 1.316 1.451 4.013 6.687 1.961 4.509 18.15 17.956 11.715 6.899 0.906 1.487 2.616 1.481 7.403 0.652 0.142 14.738 11.415 2.135 0.492 0.474 1.044 1.279 5.012 4.492 4.218 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_550_0.prm:300
 Score: 77.023, AlignedPeaks: 636244 735340 822269 935412 
0 200296 267832 288976 309146 320312 368351 388921 407099 411177 415364 424210 508919 520639 535095 536319 538905 545263 567837 596681 622514 636244 679496 692742 717386 720310 733763 735340 753269 762204 763523 765181 802869 822269 830338 840482 848514 905639 908616 917551 933610 935412 953434 988562 995566 1034575 1052457 1074139 1102983 1125557 1131915 1134501 1135725 1150181 1153088 1153695 1203084 1216845 1246610 1255456 1259643 1263721 1281899 1302469 1303186 1352562 1361674 1364518 1381844 1391675 1399370 1402988 1451626 1524408 1652810 
15.0 4.751 3.029 1.192 1.348 0.136 1.209 0.894 7.353 1.891 0.723 2.806 1.9 0.854 12.12 3.901 2.892 0.292 0.479 1.409 2.004 19.314 0.993 0.553 2.424 0.86 0.86 21.537 1.33 4.825 2.908 1.742 1.066 14.674 3.255 5.336 20.715 0.14 3.554 1.885 1.366 21.498 3.752 0.159 0.781 21.584 10.378 1.419 0.997 1.967 1.846 5.723 14.595 0.959 2.822 7.301 2.992 3.203 4.466 3.845 3.504 11.12 2.423 1.241 2.622 3.691 2.497 8.493 2.567 1.547 0.457 2.632 1.817 5.373 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_550_0.prm:302
 Score: 73.407, AlignedPeaks: 636285 735249 822226 935543 
0 195875 200379 202147 210212 225215 231725 250194 274866 277715 318328 328756 407221 411302 413166 415306 424354 426252 467448 489298 493695 535154 537884 544743 573881 575177 591983 631700 636285 666091 674115 675195 693514 696554 701639 704132 717229 721405 735249 744825 747989 760793 762322 822226 830614 840209 847332 848572 908514 910030 922834 925998 935543 953594 974269 977309 995628 1004732 1034481 1039123 1078840 1096942 1125402 1126080 1132939 1135669 1153548 1177128 1181525 1203375 1244571 1246469 1255517 1257657 1259521 1263602 1303016 1311981 1317083 1333049 1342067 1352495 1388380 1395957 1420629 1439098 1468676 1489650 1524618 1652812 
15.0 2.569 6.217 0.549 0.758 1.171 0.578 0.119 2.201 1.499 2.249 0.058 6.432 1.128 0.968 1.506 1.85 1.265 0.947 0.601 0.273 2.836 0.846 1.528 0.347 1.181 4.183 1.36 16.736 1.046 0.144 3.088 2.243 0.816 0.976 0.548 1.368 0.495 21.632 1.226 1.012 2.307 8.497 15.668 1.843 6.796 2.578 25.175 11.916 2.583 0.22 1.543 19.371 5.968 0.718 0.38 4.71 0.468 18.296 1.371 5.655 0.35 1.548 1.273 1.214 7.482 4.958 1.492 1.376 2.235 1.95 3.413 3.334 0.404 1.539 6.239 1.609 0.706 1.316 4.981 1.291 4.205 1.248 2.826 0.932 1.818 1.454 1.987 3.819 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_825_0.prm:505
 Score: 72.856, AlignedPeaks: 1036343 1293485 1406738 1493739 1778196 2079302 
0 56959 127825 235984 238967 240447 257206 262436 267256 274455 296525 308192 326196 336360 352060 353449 354234 355112 369932 371205 388729 450801 451201 455017 457479 482488 483889 509564 518431 519231 534226 538437 561991 580576 582648 618286 629575 639232 646913 656530 681886 703624 714073 738858 746942 750545 751931 767870 768391 792590 799929 811245 813320 828484 831993 861605 865122 866448 882802 884158 910152 923708 929088 939128 942555 945238 972752 974911 978205 1009338 1011674 1023119 1028284 1034761 1036343 1037555 1039663 1053532 1058154 1121410 1123389 1127836 1136460 1139725 1142752 1144834 1173344 1201151 1216861 1229732 1234624 1236612 1251633 1278494 1293485 1295503 1300395 1313266 1328976 1356783 1385293 1387375 1392515 1393667 1406738 1408717 1450010 1471973 1476595 1490464 1492572 1493739 1495366 1501843 1507008 1518453 1520789 1534282 1538039 1551922 1555203 1557375 1563880 1584889 1590999 1601039 1606419 1619975 1645969 1647325 1663679 1665005 1675301 1698134 1701643 1716807 1718883 1722746 1724263 1730198 1737537 1761736 1762257 1767107 1772190 1778196 1779582 1783185 1791269 1816054 1826503 1848241 1873597 1883214 1890889 1900552 1911841 1919262 1947479 1949551 1968136 1995901 2010896 2011696 2020563 2031732 2047639 2079302 2106839 2158923 2160224 2175015 2175894 2176687 2178068 2233603 2255672 2272921 2294144 2512117 
15.0 5.316 2.622 0.105 0.155 9.539 16.483 0.981 2.695 2.04 3.116 1.902 1.869 0.942 0.974 10.373 14.049 1.801 15.239 6.857 2.772 11.781 11.992 0.984 1.797 1.379 2.352 2.888 2.422 1.843 2.973 2.842 5.402 6.012 1.995 0.77 1.584 12.577 2.459 2.736 2.411 2.017 0.609 0.147 2.101 0.353 0.625 0.449 0.552 2.19 1.181 5.454 2.099 1.435 1.027 0.804 3.831 12.323 3.647 2.878 0.905 2.031 1.948 0.464 0.157 2.732 6.52 7.356 0.848 2.386 1.801 2.524 1.43 1.621 17.614 8.112 2.608 5.142 2.624 2.956 11.248 0.148 0.919 0.902 3.585 2.347 0.655 2.839 1.538 2.917 4.38 16.488 5.334 3.083 16.442 5.021 1.267 5.463 2.413 1.232 2.515 0.997 4.083 2.569 10.919 2.72 0.632 1.531 2.809 4.799 9.25 21.416 1.524 0.813 0.087 0.578 0.77 4.016 1.627 0.825 10.222 6.885 0.153 3.798 1.389 2.892 1.484 1.038 2.065 2.908 13.117 5.316 0.483 4.617 2.223 3.233 6.735 0.173 0.539 1.146 1.182 1.339 0.825 1.521 0.887 0.801 1.745 2.702 0.587 0.542 5.887 3.175 4.457 4.456 11.477 2.385 3.281 1.464 3.157 7.573 2.866 1.415 1.644 8.985 1.073 0.532 1.088 5.664 0.678 4.135 9.88 0.731 3.874 5.429 0.508 0.977 0.461 13.494 1.312 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:330.0, InsertsAfter: 0
 * M[1] - Mass:129042.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:330.0, InsertsAfter: 1
 * M[2] - Mass:257100.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:330.0, InsertsAfter: 0
 * M[3] - Mass:370184.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:285.0, InsertsAfter: 1
 * M[4] - Mass:457216.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:195.0, InsertsAfter: 6
 * M[5] - Mass:613317.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:165.0, InsertsAfter: 5
 * M[6] - Mass:741121.5 Overlap:3/3 LogOddsScore:5.133775021308668, SumScore:30.854, InsertsAfter: 7
 * M[7] - Mass:856437.0 Overlap:4/4 LogOddsScore:8.459356596856288, SumScore:64.314, InsertsAfter: 5
 * M[8] - Mass:955512.3333333334 Overlap:4/4 LogOddsScore:7.24861417052274, SumScore:61.903, InsertsAfter: 5
 * M[9] - Mass:1042528.0 Overlap:4/4 LogOddsScore:8.459356596856288, SumScore:69.19, InsertsAfter: 7
 * M[10] - Mass:1155604.6666666667 Overlap:4/4 LogOddsScore:8.459356596856288, SumScore:74.779, InsertsAfter: 56
ConsensusPRM: 0 129042 257100 370184 457216 613317 741121 856437 955512 1042528 1155604 Consensus: 0 129042 257100 370184 457216 613317 741121 856437 955512 1042528 1155604
De Novo: EQISRQDVSI, Merged: RVVSTIPIQHQDWMSGKEFKCKVNNKDIPSPIERTISKIKGIVRAPQVYIIPPPAEQISRKDVSI
0 156101 255169 354237 441269 542316 655400 752452 865536 993594 1130652 1258710 1373736 1559815 1690855 1777887 1834908 1963002 2092044 2239112 2367206 2527290 2655384 2754452 2868494 2982536 3110630 3225656 3338740 3435792 3522824 3619876 3732960 3862002 4018103 4119150 4232234 4319266 4447360 4560444 4688538 4745559 4858643 4957711 5113812 5184849 5281901 5409959 5509027 5672090 5785174 5898258 5995310 6092362 6189414 6260451 6389493 6517551 6630635 6717667 6873768 7001862 7116888 7215956 7302988 7416072 
30.0 330.0 390.0 435.0 465.0 555.0 645.0 645.0 645.0 645.0 645.0 660.0 645.0 615.0 450.0 390.0 375.0 315.0 240.0 90.0 105.0 90.0 225.0 225.0 270.0 315.0 390.0 390.0 405.0 405.0 405.0 420.0 420.0 450.0 390.0 240.0 240.0 240.0 165.0 105.0 135.0 165.0 165.0 165.0 300.0 300.0 300.0 300.0 390.0 390.0 330.0 330.0 330.0 330.0 330.0 330.0 330.0 328.3315668729493 283.3315668729493 193.33156687294928 163.33156687294928 30.427 47.157 45.951499999999996 49.595 52.3895 

(LEFT)Round: 0 for seed: VVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMKTSKWEKTDSFSCNV
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:36
 Score: 82.077, AlignedPeaks: 1264260 1420496 1567596 1681519 
0 168096 169980 232468 264031 279036 281902 295180 297199 303235 305294 365007 393243 396198 435263 453288 471272 506259 524263 551086 569064 593279 611304 629203 680247 698147 714170 716008 716652 734227 755120 820326 861216 867259 873226 876410 884216 915580 924476 933504 981540 989036 990130 990749 1001382 1019289 1037406 1106226 1148441 1166355 1175267 1176408 1193250 1211384 1264260 1281321 1303332 1304579 1306286 1316454 1334553 1352327 1420496 1435524 1467062 1518877 1550620 1553510 1567596 1681519 
15.0 3.152 0.008 0.27 18.189 19.439 4.402 1.799 0.754 7.256 0.949 12.768 1.282 0.049 7.03 3.006 0.614 6.079 1.643 19.197 2.856 3.469 1.869 0.807 8.632 22.845 1.227 6.772 3.019 0.045 4.964 0.67 0.033 7.026 2.671 1.906 1.509 3.013 3.636 1.885 2.629 3.034 1.324 2.232 3.006 20.651 2.565 17.727 3.143 0.342 0.168 5.941 15.454 0.077 17.419 2.342 1.372 1.218 0.65 0.625 12.668 0.573 19.762 16.275 1.767 1.19 3.275 5.561 14.896 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_625_0.prm:550
 Score: 74.686, AlignedPeaks: 989331 1088498 1187754 1244599 
0 129389 142117 210220 254861 267055 271077 332960 361498 370296 408362 460391 469230 485877 494601 538191 544106 551484 593570 594325 622799 627805 664446 665461 682445 706382 708845 720310 722361 723972 764481 770025 777472 781446 809256 815630 819584 821565 833107 863167 880286 883999 896923 920752 924820 927382 934587 947457 975528 985295 989331 1029829 1046948 1077008 1088498 1090531 1106666 1132643 1140090 1145634 1186143 1187754 1189805 1203733 1227670 1244599 1245669 1273073 1282310 1287316 1288041 1315790 1316545 1344302 1358631 1365299 1366009 1371924 1415514 1424238 1440885 1449724 1493407 1498692 1499472 1501753 1534938 1539927 1548617 1577155 1586998 1627069 1636833 1639125 1892105 
15.0 5.024 2.387 1.806 12.848 1.759 8.971 0.377 0.338 8.718 0.082 1.353 5.604 1.889 3.842 1.695 0.751 1.345 0.272 1.009 0.316 0.372 6.843 21.184 0.835 1.737 1.615 0.981 7.668 10.588 1.75 0.415 0.855 0.341 0.113 1.077 4.258 17.623 6.94 0.997 0.915 0.357 0.673 16.63 0.769 0.317 0.794 0.883 0.744 0.436 16.69 0.137 0.784 7.193 19.532 5.429 1.011 0.172 0.691 1.681 6.234 15.359 0.204 2.978 0.701 23.105 5.275 4.825 1.539 1.447 2.059 1.366 3.566 3.226 3.295 2.91 5.311 1.978 3.635 3.557 7.263 1.758 0.978 1.797 4.411 0.374 1.066 9.532 1.829 4.045 0.52 0.612 1.591 6.574 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_800_0.prm:445
 Score: 73.30100000000002, AlignedPeaks: 1456680 1555765 1612832 1759690 1873943 
0 203716 304821 322960 406141 411208 424027 439627 478270 489414 524003 532979 561216 567379 569055 589689 590296 598935 618792 656112 656859 675469 684753 737692 768960 793856 821722 822327 834333 858834 868947 879398 880030 883448 897640 920322 921150 921590 922321 936894 978454 981515 1006320 1007637 1015175 1025404 1065201 1066405 1084402 1085513 1106443 1122537 1193432 1197438 1198532 1215650 1236627 1237657 1241727 1249250 1312552 1319438 1328078 1328716 1350692 1368754 1369940 1419984 1427522 1429593 1456680 1498265 1513569 1514008 1514837 1537519 1555129 1555765 1600827 1612832 1613437 1634987 1635609 1637478 1641303 1657164 1666199 1697467 1703324 1706701 1715582 1750406 1759690 1778300 1779047 1816367 1836224 1844863 1845470 1866104 1867780 1873943 1902180 1911156 1945745 1994904 1995532 2013572 2023951 2026852 2029035 2045976 2072213 2088504 2112198 2130376 2192067 2202014 2212886 2231442 2417148 
15.0 7.79 22.041 4.791 9.703 0.95 0.72 0.277 1.351 0.96 0.735 0.845 6.302 2.212 6.209 5.707 6.186 1.27 1.296 2.613 1.433 10.205 1.879 1.167 0.43 0.144 2.021 2.349 11.604 2.817 0.096 16.407 12.332 1.545 9.422 5.835 8.579 11.099 0.218 1.956 13.797 0.653 2.615 2.407 0.829 2.259 13.734 11.438 18.677 1.642 1.64 12.006 0.795 23.103 12.357 5.152 10.339 20.404 0.222 0.307 12.148 2.024 1.035 3.173 12.954 18.313 22.755 0.797 2.08 0.512 19.041 1.489 8.83 6.096 3.485 7.77 27.496 32.082 7.392 8.368 4.86 0.027 1.355 0.719 0.471 6.233 1.98 1.314 1.204 0.188 0.109 0.932 9.657 5.169 1.647 2.706 2.468 5.512 5.514 5.646 3.396 4.153 3.319 1.283 1.875 1.0 7.226 0.027 2.606 0.206 9.766 0.193 0.618 0.032 0.501 20.635 0.641 1.045 4.197 7.568 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_700_0.prm:766
 Score: 71.92699999999999, AlignedPeaks: 1000438 1156435 1303608 1417522 
0 130908 188025 252089 278087 279117 287117 305068 376153 404106 433662 434220 435153 451995 453314 471299 483373 491116 491603 506352 508861 517440 552010 574760 592107 593312 611349 629285 657798 668595 679946 680532 698324 706415 726710 729118 735347 735982 755001 755660 783844 792778 842200 843422 857291 860773 861398 865976 870228 918093 929226 943930 944417 946491 1000438 1001313 1001990 1016488 1017187 1029329 1031426 1048342 1059380 1078484 1097206 1130465 1148414 1156435 1164200 1176383 1215140 1247508 1303608 1304624 1417522 
15.0 2.183 1.065 0.294 4.853 21.884 32.084 20.621 0.571 0.559 13.008 13.306 4.577 0.587 2.757 1.13 0.929 5.173 6.255 3.873 4.336 1.586 1.959 4.002 16.91 8.097 2.92 3.092 1.804 0.605 2.767 0.77 3.435 0.158 3.47 2.463 2.965 3.319 10.762 7.347 2.324 3.116 12.302 3.784 2.011 0.317 4.03 1.636 2.963 0.333 14.71 7.229 10.329 0.989 15.269 3.437 5.854 0.716 0.432 1.675 1.79 1.678 0.657 1.125 1.607 5.197 28.421 21.168 0.317 2.95 1.363 1.436 5.49 3.842 15.0 

SpectrumHMM Model: * M[0] - Mass:-614179.5 Overlap:2/3 LogOddsScore:4.138885782823805, SumScore:51.281000000000006, InsertsAfter: 49
 * M[1] - Mass:0.0 Overlap:2/5 LogOddsScore:3.704163115534604, SumScore:60.0, InsertsAfter: 112
 * M[2] - Mass:99068.0 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:111.729, InsertsAfter: 15
 * M[3] - Mass:198147.33333333334 Overlap:3/5 LogOddsScore:6.41607005251406, SumScore:92.082, InsertsAfter: 23
 * M[4] - Mass:255190.71428571426 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:124.298, InsertsAfter: 3
 * M[5] - Mass:402237.85714285716 Overlap:5/5 LogOddsScore:8.658986165564308, SumScore:105.04299999999999, InsertsAfter: 21
 * M[6] - Mass:516269.5714285714 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:109.153, InsertsAfter: 9
 * M[7] - Mass:613319.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:75.0, InsertsAfter: 3
 * M[8] - Mass:671062.0 Overlap:1/3 LogOddsScore:0.21623641951080008, SumScore:9.766, InsertsAfter: 5
 * M[9] - Mass:785366.0 Overlap:2/3 LogOddsScore:4.392023418904327, SumScore:75.0, InsertsAfter: 5
 * M[10] - Mass:898450.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:75.0, InsertsAfter: 4
 * M[11] - Mass:985482.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:90.0, InsertsAfter: 0
ConsensusPRM: -614179 0 99068 198147 255190 402237 516269 613319 671062 785366 898450 985482 Consensus: -614179 0 99068 198147 255190 402237 516269 613319 671062 785366 898450 985482
De Novo: VVGFNP[172.047]IS, Merged: VVGFNPGDISVEWTSNGHTEENYKDTAPVIDSDGSYFIYSKINMKTSKWEKTDSFSCNV
-614179 0 99068 198147 255190 402237 516269 613319 670340 671062 785366 898450 985482 1084550 1213592 1399671 1500718 1587750 1701792 1758813 1895871 1996918 2125960 2255002 2369044 2532107 2660201 2775227 2876274 2947311 3044363 3143431 3256515 3371541 3458573 3573599 3630620 3717652 3880715 4027783 4140867 4303930 4390962 4519056 4632140 4746182 4877222 5005316 5106363 5193395 5321489 5507568 5636610 5764704 5865751 5980777 6067809 6214877 6301909 6461993 6576035 6675103 
51.281000000000006 60.0 85.86449999999999 76.041 99.649 90.0215 92.07650000000001 75.0 75.0 9.766 75.0 75.0 90.0 90.0 90.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 75.0 180.0 225.0 255.0 285.0 285.0 285.0 285.0 285.0 285.0 315.0 270.0 225.0 225.0 210.0 210.0 270.0 240.0 225.0 225.0 225.0 210.0 225.0 225.0 270.0 210.0 210.0 210.0 210.0 210.0 195.0 195.0 195.0 195.0 195.0 30.0 30.0 30.0 30.0 30.0 
(RIGHT)Round: 0 for seed: VVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMKTSKWEKTDSFSCNV
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_500_0.prm:62
 Score: 126.289, AlignedPeaks: 0 216147 303124 450119 537157 811287 
0 174238 215050 216147 234088 303124 343557 370255 387337 405064 405690 449141 450119 490275 522635 525588 531623 537157 544493 577300 595335 621774 622574 623331 630668 640073 657271 706323 724319 725348 742290 754222 756009 793356 811287 821429 853218 881238 908354 1009421 
15.0 8.695 1.777 30.976 18.93 18.041 1.08 6.871 3.29 2.653 1.693 1.132 15.822 2.492 7.658 1.017 3.404 9.396 1.689 1.622 2.226 12.273 11.448 2.602 4.648 10.643 6.334 0.813 13.979 1.47 1.629 11.893 1.019 6.843 22.054 8.982 8.021 2.24 0.496 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Trypsin_0_0_500_0.prm:56
 Score: 108.55499999999999, AlignedPeaks: 0 101045 216074 303102 450171 537203 811363 
0 101045 216074 234080 303102 370102 449167 450171 490231 522720 525524 531192 531678 537203 573188 595270 621751 623266 630256 630758 640212 657212 724332 725334 740367 794356 811363 853323 908504 1009423 
15.0 1.282 28.732 0.631 15.336 4.079 0.596 11.237 0.99 4.481 0.236 1.929 4.078 7.06 0.119 2.487 0.193 2.818 1.937 4.206 1.7 2.426 3.124 1.88 0.642 0.09 14.908 4.061 0.701 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_575_0.prm:733
 Score: 81.59200000000001, AlignedPeaks: 502258 631194 759319 860479 975548 1062549 1209562 1296649 1570768 
0 170243 174234 187641 188211 206127 234165 235996 272755 285041 315869 333711 338301 387278 396855 478149 489393 500519 502258 504842 506576 514116 518982 577280 587545 591227 618249 623819 631194 648243 677251 678509 724279 726567 736278 759319 765590 777533 790977 793502 799602 806433 811288 824450 860479 874349 878517 893388 912496 926366 943358 962395 975548 980412 987243 993476 999552 1027492 1050567 1051350 1060278 1062549 1138602 1153380 1155638 1163026 1168596 1203116 1205768 1209562 1211681 1217703 1253803 1259575 1272729 1280269 1282003 1284592 1286326 1296649 1297452 1299087 1308013 1308696 1356440 1372439 1387665 1389990 1393057 1399567 1407243 1425076 1470987 1490050 1501804 1532567 1550849 1552680 1567548 1570768 1580720 1598634 1612611 1768835 
15.0 1.746 2.428 4.209 13.669 5.428 0.383 0.98 1.498 0.712 17.504 2.351 0.037 0.181 0.533 3.045 1.909 0.822 11.804 0.238 1.198 0.094 1.899 1.993 0.816 0.864 1.121 1.777 14.941 3.432 0.587 0.733 4.528 0.209 0.665 11.786 1.277 4.758 0.037 7.775 0.086 7.098 14.512 1.72 11.862 1.073 0.725 4.804 0.302 10.814 1.659 0.482 14.396 4.48 0.179 15.493 2.122 19.16 0.689 3.265 0.087 5.845 1.142 0.509 16.971 0.123 0.792 0.351 0.235 7.89 0.782 4.87 2.02 0.211 0.191 1.889 1.567 13.772 1.847 1.546 2.112 0.129 1.564 3.384 1.266 0.725 1.97 2.834 1.581 3.481 0.424 0.509 12.531 0.564 0.994 4.976 1.044 1.065 0.502 1.522 8.16 6.65 4.709 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:869
 Score: 76.999, AlignedPeaks: 0 234164 321109 595233 
0 137107 146799 234164 245274 251871 320093 321109 394348 398409 430211 431290 449317 451050 467354 483237 484180 518860 554836 559227 560312 570906 578319 595233 596372 633005 635195 638043 652110 654406 660385 663496 680766 689783 691425 701375 710530 718131 748302 783214 784308 788699 797734 816096 824675 854237 859343 876181 877472 895200 905468 912204 915418 925435 945125 960255 1022423 1023442 1024367 1032127 1040401 1098245 1109367 1110238 1137350 1178759 1196736 1197426 1325524 
15.0 1.197 5.706 27.86 2.138 3.576 1.4 15.538 2.459 0.082 0.051 11.293 4.708 1.219 1.658 3.086 15.401 0.236 0.186 2.053 11.69 1.879 5.008 3.601 3.225 0.311 0.773 0.966 0.449 0.866 0.758 0.148 2.985 5.986 1.982 1.518 1.578 0.323 3.669 15.078 0.4 0.362 8.056 0.789 0.16 0.123 1.056 0.673 0.061 1.599 0.637 17.269 1.19 2.098 0.431 1.023 0.289 0.639 0.78 0.571 5.146 10.326 24.403 6.133 3.588 1.879 8.351 7.786 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_525_0.prm:143
 Score: 74.875, AlignedPeaks: 0 303190 697287 811414 
0 156244 174307 184210 211362 225436 241216 245328 258838 291196 303190 339983 357946 400136 405948 414669 433197 437339 454228 463616 468152 471255 471864 511830 513270 523384 529389 530318 531892 551429 567197 584119 586339 600222 601711 610293 632166 679282 682093 695417 697287 699404 713427 714246 715362 723809 732728 749557 792432 793659 796749 808966 810418 811414 812229 827625 828440 829412 846195 847422 907182 924492 925608 926427 940450 942521 944437 949320 957761 960572 998844 1007688 1029560 1039632 1053515 1055735 1072657 1088425 1104880 1107962 1109536 1110465 1126583 1128024 1167990 1168599 1177395 1182775 1185626 1194585 1225185 1233906 1239718 1281983 1283833 1291008 1299871 1336664 1348658 1381054 1382474 1383203 1447618 1465531 1621844 
15.0 0.511 9.621 0.582 0.873 1.703 2.449 5.421 17.407 0.886 1.723 1.046 14.477 4.254 0.464 0.334 0.879 1.128 0.219 0.774 0.534 8.277 6.2 1.344 8.918 0.283 0.274 0.161 1.318 1.234 1.969 2.046 3.357 0.415 2.485 3.537 0.652 1.956 1.358 2.534 25.432 2.222 0.716 16.108 8.88 0.396 13.187 4.862 1.011 3.062 0.983 0.717 22.377 17.72 3.695 4.286 18.878 25.364 1.266 1.231 9.389 4.199 14.058 0.794 0.377 31.773 0.974 0.623 0.566 7.139 0.69 0.566 1.087 1.582 0.58 1.506 0.834 0.221 1.015 0.013 1.46 1.277 17.267 0.805 4.243 6.695 1.237 2.715 1.988 0.429 1.565 1.326 5.234 9.304 0.276 4.982 5.5 2.445 1.691 9.282 1.47 3.224 0.023 14.374 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:3/3 LogOddsScore:5.640050293469712, SumScore:221.804, InsertsAfter: 9
 * M[1] - Mass:128989.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:209.941, InsertsAfter: 6
 * M[2] - Mass:257123.5 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:236.786, InsertsAfter: 8
 * M[3] - Mass:358191.5 Overlap:4/5 LogOddsScore:6.200216864665374, SumScore:208.144, InsertsAfter: 9
 * M[4] - Mass:473247.5 Overlap:5/5 LogOddsScore:11.58674629039245, SumScore:269.104, InsertsAfter: 10
 * M[5] - Mass:560254.6666666666 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:234.222, InsertsAfter: 15
 * M[6] - Mass:707289.5 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:64.949, InsertsAfter: 18
 * M[7] - Mass:794332.6666666666 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:48.002, InsertsAfter: 29
 * M[8] - Mass:954425.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 18
 * M[9] - Mass:1068470.1666666665 Overlap:5/5 LogOddsScore:9.363453319736813, SumScore:68.48400000000001, InsertsAfter: 9
 * M[10] - Mass:1167535.0 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 0
 * M[11] - Mass:1266561.8 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
ConsensusPRM: 0 128989 257123 358191 473247 560254 707289 794332 954425 1068470 1167535 1266561 Consensus: 0 128989 257123 358191 473247 560254 707289 794332 954425 1068470 1167535 1266561
De Novo: EKTDSFSCNVV, Merged: VVGFNPGDISVEWTSNGHTEENYKDTAPVIDSDGSYFIYSKINMKTSKWEKTDSFSCNVV
0 99068 198136 255157 402225 516267 613319 670340 785366 898450 985482 1084550 1213592 1399671 1500718 1587750 1701792 1758813 1895871 1996918 2125960 2255002 2369044 2532107 2660201 2775227 2876274 2947311 3044363 3143431 3256515 3371541 3458573 3573599 3630620 3717652 3880715 4027783 4140867 4303930 4390962 4519056 4632140 4746182 4877222 5005316 5106363 5193395 5321489 5507568 5636610 5764704 5865751 5980777 6067809 6214877 6301909 6461993 6576035 6675103 6774129 
60.0 60.0 60.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 90.0 90.0 90.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 75.0 180.0 225.0 255.0 285.0 285.0 285.0 285.0 285.0 285.0 315.0 270.0 225.0 225.0 210.0 210.0 270.0 240.0 225.0 225.0 225.0 210.0 225.0 225.0 270.0 210.0 210.0 210.0 210.0 215.902 202.47050000000002 215.893 199.90356687294928 232.052 214.611 47.4745 39.001000000000005 24.994700618847887 49.242000000000004 24.994700618847887 45.0 
(RIGHT)Round: 1 for seed: VVGFNPGDISVEWTSNGHTEENYKDTAPVIDSDGSYFIYSKINMKTSKWEKTDSFSCNVV
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:869
 Score: 76.999, AlignedPeaks: 0 234164 321109 595233 
0 137107 146799 234164 245274 251871 320093 321109 394348 398409 430211 431290 449317 451050 467354 483237 484180 518860 554836 559227 560312 570906 578319 595233 596372 633005 635195 638043 652110 654406 660385 663496 680766 689783 691425 701375 710530 718131 748302 783214 784308 788699 797734 816096 824675 854237 859343 876181 877472 895200 905468 912204 915418 925435 945125 960255 1022423 1023442 1024367 1032127 1040401 1098245 1109367 1110238 1137350 1178759 1196736 1197426 1325524 
15.0 1.197 5.706 27.86 2.138 3.576 1.4 15.538 2.459 0.082 0.051 11.293 4.708 1.219 1.658 3.086 15.401 0.236 0.186 2.053 11.69 1.879 5.008 3.601 3.225 0.311 0.773 0.966 0.449 0.866 0.758 0.148 2.985 5.986 1.982 1.518 1.578 0.323 3.669 15.078 0.4 0.362 8.056 0.789 0.16 0.123 1.056 0.673 0.061 1.599 0.637 17.269 1.19 2.098 0.431 1.023 0.289 0.639 0.78 0.571 5.146 10.326 24.403 6.133 3.588 1.879 8.351 7.786 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_525_0.prm:143
 Score: 74.875, AlignedPeaks: 0 303190 697287 811414 
0 156244 174307 184210 211362 225436 241216 245328 258838 291196 303190 339983 357946 400136 405948 414669 433197 437339 454228 463616 468152 471255 471864 511830 513270 523384 529389 530318 531892 551429 567197 584119 586339 600222 601711 610293 632166 679282 682093 695417 697287 699404 713427 714246 715362 723809 732728 749557 792432 793659 796749 808966 810418 811414 812229 827625 828440 829412 846195 847422 907182 924492 925608 926427 940450 942521 944437 949320 957761 960572 998844 1007688 1029560 1039632 1053515 1055735 1072657 1088425 1104880 1107962 1109536 1110465 1126583 1128024 1167990 1168599 1177395 1182775 1185626 1194585 1225185 1233906 1239718 1281983 1283833 1291008 1299871 1336664 1348658 1381054 1382474 1383203 1447618 1465531 1621844 
15.0 0.511 9.621 0.582 0.873 1.703 2.449 5.421 17.407 0.886 1.723 1.046 14.477 4.254 0.464 0.334 0.879 1.128 0.219 0.774 0.534 8.277 6.2 1.344 8.918 0.283 0.274 0.161 1.318 1.234 1.969 2.046 3.357 0.415 2.485 3.537 0.652 1.956 1.358 2.534 25.432 2.222 0.716 16.108 8.88 0.396 13.187 4.862 1.011 3.062 0.983 0.717 22.377 17.72 3.695 4.286 18.878 25.364 1.266 1.231 9.389 4.199 14.058 0.794 0.377 31.773 0.974 0.623 0.566 7.139 0.69 0.566 1.087 1.582 0.58 1.506 0.834 0.221 1.015 0.013 1.46 1.277 17.267 0.805 4.243 6.695 1.237 2.715 1.988 0.429 1.565 1.326 5.234 9.304 0.276 4.982 5.5 2.445 1.691 9.282 1.47 3.224 0.023 14.374 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_800_0.prm:90
 Score: 74.381, AlignedPeaks: 988476 1116671 1419670 1653781 2027286 
0 127730 163406 248411 250574 266812 278244 279166 296070 318151 336151 353562 380873 408916 423761 426872 431218 445260 449310 459271 467164 494514 509883 537192 549650 558515 580501 646072 654488 690928 700750 701361 710994 736449 737890 772202 775439 784709 790504 822744 827344 846142 847675 862619 871734 887509 898412 901188 917714 918470 926771 927554 953168 970497 986604 988476 1004880 1006558 1018533 1027298 1036026 1036680 1038291 1045501 1047492 1070673 1116186 1116671 1131284 1132079 1140214 1141671 1143436 1159752 1160522 1174407 1222894 1247637 1248407 1264723 1266488 1267269 1267945 1276080 1276875 1291488 1291973 1360667 1371479 1372133 1380861 1417516 1419670 1421555 1428430 1437662 1471725 1480605 1481395 1489689 1490445 1509747 1520650 1545540 1560484 1580815 1585415 1616835 1617655 1621148 1622834 1623450 1627232 1632720 1635957 1647860 1653781 1670269 1671710 1697165 1698075 1706798 1707400 1717231 1743468 1753671 1762087 1827658 1849644 1858509 1870821 1884196 1898276 1913645 1948888 1958849 1959458 1962899 1976940 1984398 1999243 2027286 2047897 2072036 2090007 2110875 2112089 2124947 2128993 2157585 2158975 2177273 2232372 2262568 2390148 
15.0 10.72 0.973 0.573 0.244 0.789 1.804 2.288 1.693 0.188 16.374 2.151 1.206 12.719 0.441 1.872 3.689 0.998 8.644 0.883 1.123 1.269 0.419 11.58 2.158 3.969 3.889 1.365 1.708 3.294 7.142 7.35 0.028 2.361 4.543 1.18 1.987 1.95 2.659 5.858 2.97 2.938 1.645 1.243 2.559 3.715 4.578 0.67 0.187 2.825 5.977 1.366 0.466 4.788 6.759 24.901 3.372 5.863 1.493 6.822 5.766 5.101 0.437 0.792 9.983 0.006 15.733 17.663 1.403 2.696 2.594 1.239 4.787 2.663 7.464 1.743 0.783 8.69 0.795 3.424 1.778 0.798 4.233 0.183 2.272 15.157 15.157 11.852 6.45 6.245 10.188 0.515 28.185 4.225 0.488 12.158 2.438 1.396 8.635 10.019 5.885 7.036 1.477 2.161 3.125 0.935 5.769 2.844 5.832 0.952 0.676 1.68 0.157 0.298 0.881 1.641 2.075 3.023 0.537 1.334 4.421 6.86 6.813 1.448 1.007 2.236 3.46 5.012 5.986 3.317 12.177 6.176 0.783 2.287 1.963 7.565 0.331 2.258 1.505 1.094 7.856 1.557 0.554 12.784 0.076 1.37 10.876 0.531 0.29 0.095 9.293 2.453 1.748 6.63 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:202.47050000000002, InsertsAfter: 0
 * M[1] - Mass:128094.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:215.893, InsertsAfter: 0
 * M[2] - Mass:229141.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:199.90356687294928, InsertsAfter: 0
 * M[3] - Mass:344167.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:232.052, InsertsAfter: 0
 * M[4] - Mass:431199.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:214.611, InsertsAfter: 0
 * M[5] - Mass:578267.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:47.4745, InsertsAfter: 0
 * M[6] - Mass:665299.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:39.001000000000005, InsertsAfter: 0
 * M[7] - Mass:825383.0 Overlap:2/2 LogOddsScore:1.808193445761047, SumScore:24.994700618847887, InsertsAfter: 0
 * M[8] - Mass:939425.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:49.242000000000004, InsertsAfter: 0
 * M[9] - Mass:1038493.0 Overlap:2/2 LogOddsScore:1.808193445761047, SumScore:24.994700618847887, InsertsAfter: 0
 * M[10] - Mass:1137519.0 Overlap:2/2 LogOddsScore:4.229678298428144, SumScore:45.0, InsertsAfter: 0
ConsensusPRM: 0 128094 229141 344167 431199 578267 665299 825383 939425 1038493 1137519 Consensus: 0 128094 229141 344167 431199 578267 665299 825383 939425 1038493 1137519
De Novo: KTDSFSCNVV, Merged: VVGFNPGDISVEWTSNGHTEENYKDTAPVIDSDGSYFIYSKINMKTSKWEKTDSFSCNVV
0 99068 198136 255157 402225 516267 613319 670340 785366 898450 985482 1084550 1213592 1399671 1500718 1587750 1701792 1758813 1895871 1996918 2125960 2255002 2369044 2532107 2660201 2775227 2876274 2947311 3044363 3143431 3256515 3371541 3458573 3573599 3630620 3717652 3880715 4027783 4140867 4303930 4390962 4519056 4632140 4746182 4877222 5005316 5106363 5193395 5321489 5507568 5636610 5764704 5865751 5980777 6067809 6214877 6301909 6461993 6576035 6675103 6774129 
60.0 60.0 60.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 90.0 90.0 90.0 60.0 60.0 60.0 60.0 60.0 60.0 60.0 75.0 180.0 225.0 255.0 285.0 285.0 285.0 285.0 285.0 285.0 315.0 270.0 225.0 225.0 210.0 210.0 270.0 240.0 225.0 225.0 225.0 210.0 225.0 225.0 270.0 210.0 210.0 210.0 210.0 215.902 202.47050000000002 215.893 199.90356687294928 232.052 214.611 47.4745 39.001000000000005 24.994700618847887 49.242000000000004 24.994700618847887 45.0 

(LEFT)Round: 0 for seed: HEGLKNYYLKKTISRSPG
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:449
 Score: 92.40799999999999, AlignedPeaks: 1039396 1176601 1305695 1475640 1603817 1718002 1881122 2043948 
0 101134 112687 130574 147547 232120 233674 234114 283186 300860 311423 317187 344051 361871 412249 457584 458142 482296 509575 511443 516547 567096 568346 569157 582716 583485 585101 586319 587941 638526 643935 686598 688383 690380 697951 699814 715244 717322 738621 755082 756240 757309 759409 790096 802189 867041 869394 872105 883267 885358 886729 887493 903071 903819 906730 947447 957206 974636 980413 981161 990544 1022494 1039396 1071415 1080798 1081546 1087323 1104034 1104753 1121398 1147038 1147817 1174466 1175230 1176601 1181406 1189854 1192565 1194918 1259770 1268850 1271863 1304650 1305695 1306877 1323338 1344637 1362145 1364008 1373576 1389760 1409048 1412041 1418024 1423433 1424101 1472458 1474830 1475640 1492802 1493613 1494863 1545412 1550516 1552384 1579663 1603817 1604377 1615021 1621687 1649710 1673594 1674556 1674980 1700088 1718002 1726698 1744772 1761104 1778773 1784873 1812784 1827845 1828284 1829842 1855816 1881122 1914412 1915850 2043948 
15.0 4.0 11.686 9.147 5.911 3.328 9.504 9.505 2.722 23.01 2.564 3.566 10.32 6.843 0.31 17.785 18.873 2.104 2.125 2.277 0.583 2.822 2.638 4.524 0.205 2.711 4.579 2.706 0.409 0.028 1.341 0.703 7.522 0.83 0.946 0.694 1.962 2.825 2.501 2.898 14.001 1.5 1.804 1.59 1.531 6.348 1.498 0.781 2.466 3.728 3.912 4.877 0.158 0.672 0.322 2.507 0.114 1.433 0.382 1.056 2.764 13.575 15.591 0.29 0.502 0.377 2.769 1.869 0.623 1.185 3.851 1.555 0.824 2.081 1.663 8.058 0.045 3.249 8.358 2.154 0.07 2.359 4.569 21.214 7.387 5.821 0.514 3.653 1.106 8.208 2.176 0.04 1.228 5.596 2.096 1.058 0.419 3.423 0.814 5.208 5.397 14.126 1.591 2.627 2.435 0.095 8.86 5.43 0.71 0.395 3.128 0.28 0.424 0.474 1.144 12.163 0.899 3.231 1.83 10.061 2.085 3.049 3.092 3.59 1.775 1.352 2.103 2.195 5.411 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:448
 Score: 91.331, AlignedPeaks: 1039532 1176718 1305650 1475408 1603856 1717830 1880678 2043948 
0 100648 112769 130716 146855 232149 233763 276983 283218 300787 301297 344129 361687 387211 405216 456833 458105 511353 511859 566105 585234 585930 586551 589375 603314 613545 643882 692396 715264 715581 738000 754374 756302 759307 801928 820431 866528 869434 880586 882250 883490 885226 886260 887299 887684 902183 914110 941094 965621 974595 980655 983708 990585 990897 1022426 1039532 1087364 1096338 1104407 1121620 1147849 1174275 1176718 1178469 1179709 1180927 1181373 1181628 1192525 1195431 1241528 1259396 1260031 1305650 1307585 1316536 1323959 1346378 1363801 1386057 1408286 1409149 1412058 1418077 1423661 1423950 1434751 1444265 1448414 1458645 1472584 1474797 1475408 1476029 1476724 1492712 1493952 1495854 1542137 1550100 1550606 1597819 1603856 1621707 1649569 1656743 1674748 1692823 1700272 1717830 1744849 1760663 1761172 1778741 1784976 1812740 1828214 1829810 1855834 1880678 1915104 1931242 2043948 
15.0 4.572 12.025 9.398 5.081 3.741 8.291 0.182 2.697 21.214 20.208 3.845 7.712 1.512 0.324 0.509 16.897 2.687 0.917 1.695 9.422 5.589 5.362 0.121 3.071 1.547 1.41 1.015 2.752 2.832 3.435 4.334 16.278 0.605 1.902 1.885 1.149 1.557 0.024 3.433 2.238 9.43 1.567 3.421 3.965 1.503 0.152 1.492 0.987 2.953 1.691 2.779 1.868 2.499 9.134 11.14 0.564 2.309 1.052 0.248 1.538 2.21 5.728 2.051 2.732 4.763 8.553 8.553 2.955 3.083 0.172 1.449 3.827 24.474 3.214 0.332 14.405 0.481 3.025 0.806 2.989 0.293 1.362 6.472 1.037 1.005 0.449 1.974 0.88 4.9 0.274 1.957 5.622 4.903 9.522 1.092 4.987 5.053 0.034 3.221 2.441 5.746 3.395 0.891 2.023 4.488 5.813 0.474 0.973 9.379 1.24 4.512 1.755 9.905 1.826 1.839 3.098 3.358 0.759 1.593 2.412 5.228 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:445
 Score: 78.09299999999999, AlignedPeaks: 1039448 1305544 1475449 1603512 1717663 1881210 2043845 
0 100685 113221 130615 147483 233792 277062 283212 299839 301107 317156 317609 327100 344192 360885 362247 387262 457799 480879 500076 503067 505339 511265 548269 568075 568868 569124 586101 586406 587208 643825 652724 705045 715133 733318 737945 744360 756309 790098 793200 802035 849804 872123 882347 885255 885527 887259 913432 932604 940605 949342 965620 974317 1000541 1022407 1039448 1061314 1081270 1087538 1104197 1104669 1121250 1129251 1147814 1174596 1180847 1181481 1189732 1212051 1259820 1260100 1271757 1305544 1317495 1323911 1346723 1361606 1386087 1389448 1409131 1412001 1418030 1423799 1434693 1444207 1472639 1474647 1475449 1475755 1492731 1492987 1493781 1513586 1550591 1556516 1558788 1561779 1575655 1592561 1598631 1603512 1604070 1662586 1674593 1699608 1700970 1717663 1734756 1744246 1744699 1760748 1778643 1784793 1812730 1828078 1829806 1855628 1881210 1914372 1915316 1931240 2043845 
15.0 4.672 12.19 8.782 6.168 7.984 0.739 1.97 1.014 19.856 2.762 4.175 0.121 1.972 1.589 4.93 0.002 13.058 2.395 0.982 0.076 0.606 2.48 3.877 7.505 2.641 2.547 4.257 6.692 0.101 0.713 0.033 2.161 2.075 0.077 3.778 0.744 15.084 0.443 1.422 1.096 0.162 0.335 1.016 2.051 0.313 4.138 2.763 5.715 0.027 0.033 0.161 2.095 5.849 3.157 5.612 6.69 0.335 0.535 1.471 1.823 0.58 2.573 1.678 1.504 1.872 3.141 0.904 0.435 2.476 3.427 4.113 24.916 0.726 9.668 2.486 0.069 1.472 0.045 0.063 1.083 5.91 1.7 1.72 1.529 0.37 2.337 4.792 1.273 9.003 10.759 13.466 1.115 3.109 2.784 0.05 2.977 0.491 2.36 5.697 4.015 4.016 0.999 3.263 0.281 0.838 7.01 0.982 4.247 4.249 2.034 8.405 2.053 2.989 2.714 1.132 0.972 1.748 2.237 2.496 4.501 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_950_0.prm:50
 Score: 77.566, AlignedPeaks: 1396630 1525837 1582779 1695906 1823911 
0 128322 216188 239830 244206 275541 312234 313281 325224 337899 338588 341910 343133 346121 353365 407119 425037 427406 432125 440416 442628 455896 459115 470450 471330 484127 504314 539897 548919 568442 584258 603705 604399 610536 613431 640254 642105 672375 681510 689418 732746 741987 755370 773414 782608 791284 791970 830236 838819 839457 848068 894148 902845 903636 911875 912557 940382 951708 962285 1012208 1015402 1035553 1041030 1046436 1053354 1068292 1079435 1095365 1097452 1098205 1099627 1116232 1125237 1127362 1140352 1208470 1214726 1221438 1224378 1225456 1226340 1227549 1231180 1239367 1243509 1261507 1282429 1283134 1287671 1289726 1300576 1323591 1338580 1352587 1353661 1382276 1395525 1396630 1410540 1436001 1437557 1440802 1457691 1463671 1480560 1481556 1483805 1485361 1524635 1525837 1533365 1567701 1568775 1582779 1597771 1620786 1631636 1633691 1638228 1638933 1677853 1681995 1690182 1693813 1695022 1695906 1696984 1699924 1706636 1712838 1781010 1794000 1796028 1797035 1805130 1821735 1823157 1823911 1825997 1841927 1853070 1868008 1874925 1880332 1885809 1897007 1905960 1959077 1969654 1980980 2008805 2009487 2017726 2018517 2027214 2040107 2073293 2081905 2082543 2091126 2129392 2130078 2138754 2147948 2165992 2179375 2188616 2231944 2239852 2248987 2279257 2281108 2307931 2310826 2316963 2317657 2337104 2352920 2372443 2381465 2437235 2450032 2450912 2462318 2465466 2478734 2480946 2489237 2493956 2496325 2514243 2575303 2578229 2582774 2583463 2608081 2609128 2640358 2645821 2677156 2705174 2903352 
15.0 3.153 2.548 3.17 6.219 1.358 2.88 2.89 1.014 0.825 0.498 0.754 5.152 9.604 3.491 1.14 2.35 1.251 1.914 0.737 4.983 1.387 8.644 6.059 11.081 1.828 3.728 1.69 3.168 2.523 1.148 3.058 2.435 2.984 4.431 2.447 2.929 7.806 2.515 9.311 4.514 1.567 2.392 2.985 2.732 3.55 0.81 2.279 1.549 2.876 0.629 0.834 2.159 1.763 2.838 3.073 3.181 3.077 3.012 1.027 1.679 2.714 4.525 0.554 2.539 0.408 1.539 3.328 22.138 15.193 0.35 15.064 5.909 2.374 1.906 6.622 2.702 2.531 7.352 15.557 9.289 5.537 2.49 3.628 8.649 5.72 4.064 3.602 0.906 1.531 3.724 3.067 11.423 0.983 4.284 0.446 2.676 10.317 5.605 2.064 6.137 6.238 3.489 1.706 4.807 4.95 6.308 0.977 5.935 1.705 1.704 3.527 2.608 17.901 2.208 1.269 0.256 1.116 3.938 3.179 7.819 2.102 2.349 5.771 13.565 19.266 3.681 3.882 2.241 11.92 1.497 2.068 4.713 0.09 8.331 2.679 22.106 28.377 3.162 11.487 0.451 2.693 0.384 2.838 0.635 2.969 1.753 1.718 3.402 2.704 5.685 6.509 2.85 2.38 2.343 4.883 2.249 3.601 3.679 2.836 2.944 3.483 4.681 3.213 2.724 3.868 4.105 9.591 3.537 9.649 1.291 1.032 1.391 0.633 1.654 1.624 4.242 1.332 4.77 0.783 0.833 7.583 1.2 10.715 0.89 0.434 4.442 0.649 0.409 1.246 0.142 10.532 7.676 0.332 0.022 0.506 0.77 1.21 0.924 5.308 2.444 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_625_0.prm:174
 Score: 75.969, AlignedPeaks: 902610 1039613 1168491 1225475 1466574 
0 159840 173848 208558 231104 275279 349400 374287 377812 412363 413148 442281 457350 487408 498020 510571 533658 570141 591696 617279 644312 656176 671360 696245 698432 699178 755402 766095 772537 774695 775391 783642 815321 824903 826596 844499 845299 851236 865807 875038 882042 884480 902610 909299 936300 938277 956606 967318 985624 1021314 1039202 1039613 1041882 1048886 1072653 1079425 1097328 1099021 1099682 1108603 1148533 1149229 1151387 1157829 1168491 1224746 1225475 1267748 1294427 1300573 1310567 1311229 1320082 1332228 1339659 1348508 1353783 1390266 1413353 1421776 1425904 1431088 1436516 1463805 1466574 1481643 1510778 1511561 1530106 1538588 1543003 1546112 1549534 1574524 1648544 1649806 1666693 1680648 1681815 1692820 1693768 1695635 1701777 1731614 1750076 1764084 1768622 1905914 
15.0 1.963 3.025 2.094 1.738 14.51 1.23 8.105 5.767 9.029 11.843 0.929 5.4 0.613 1.391 2.775 1.447 0.076 3.508 0.788 0.478 0.845 0.092 1.921 13.677 8.876 16.562 1.787 1.832 5.087 0.992 0.333 0.653 0.703 8.87 3.756 0.117 6.737 0.426 1.288 1.078 14.64 1.788 0.997 1.702 15.988 1.926 0.345 13.177 0.091 19.069 20.481 0.14 1.199 9.93 0.762 8.648 2.86 2.931 0.094 0.843 6.906 3.531 0.05 27.013 11.85 19.971 0.255 2.508 0.091 0.596 1.422 0.848 4.963 0.78 1.185 0.56 0.412 2.706 0.365 1.48 1.268 4.76 4.545 6.716 0.438 5.002 4.621 0.465 1.437 0.228 7.32 11.895 4.501 13.727 2.644 1.657 1.83 1.532 2.02 1.099 1.966 4.418 0.375 5.47 1.883 3.188 15.0 

SpectrumHMM Model: * M[0] - Mass:-1039458.6666666667 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
 * M[1] - Mass:-908823.6666666666 Overlap:3/3 LogOddsScore:2.7122901686415704, SumScore:27.327, InsertsAfter: 6
 * M[2] - Mass:-738558.818181818 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:64.08000000000001, InsertsAfter: 15
 * M[3] - Mass:-695334.6666666666 Overlap:3/3 LogOddsScore:2.7122901686415704, SumScore:16.137, InsertsAfter: 6
 * M[4] - Mass:-581443.3333333334 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:48.827999999999996, InsertsAfter: 10
 * M[5] - Mass:-283175.0 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.363, InsertsAfter: 57
 * M[6] - Mass:0.0 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:62.343, InsertsAfter: 60
 * M[7] - Mass:137162.5 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:37.391, InsertsAfter: 26
 * M[8] - Mass:266148.99999999994 Overlap:5/5 LogOddsScore:10.57419574607036, SumScore:100.604, InsertsAfter: 25
 * M[9] - Mass:322830.3333333333 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:33.653, InsertsAfter: 11
 * M[10] - Mass:435787.3333333334 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:43.837, InsertsAfter: 33
 * M[11] - Mass:564393.0000000001 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:46.271, InsertsAfter: 30
 * M[12] - Mass:678383.5 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:73.552, InsertsAfter: 18
 * M[13] - Mass:841514.8333333333 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:80.444, InsertsAfter: 29
 * M[14] - Mass:1004371.846153846 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:135.0, InsertsAfter: 7
 * M[15] - Mass:1117551.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:105.0, InsertsAfter: 0
 * M[16] - Mass:1245645.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:105.0, InsertsAfter: 0
ConsensusPRM: -1039458 -908823 -738558 -695334 -581443 -283175 0 137162 266148 322830 435787 564393 678383 841514 1004371 1117551 1245645 Consensus: -1039458 -908823 -738558 -695334 -581443 -283175 0 137162 266148 322830 435787 564393 678383 841514 1004371 1117551 1245645
De Novo: [283.175]HEGIENYYIK, Merged: [283.175]HEGIENYYIKKTISRSPG
-1039458 -908823 -738558 -695334 -581443 -283175 0 137162 266148 322830 435787 564393 678383 841514 1004371 1117551 1245645 1373739 1474786 1587870 1674902 1831003 1918035 2015087 2072108 
45.0 27.327 64.08000000000001 16.137 48.827999999999996 45.363 46.1715 33.695499999999996 65.30199999999999 31.8265 36.9185 38.1355 59.276 77.72200000000001 112.5 105.0 105.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 

(LEFT)Round: 1 for seed: [283.175]HEGIENYYIKKTISRSPG
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:449
 Score: 112.67099999999999, AlignedPeaks: 756240 1039396 1176601 1305695 1362145 1474830 1603817 1718002 1881122 2043948 
0 101134 112687 130574 147547 232120 233674 234114 283186 300860 311423 317187 344051 361871 412249 457584 458142 482296 509575 511443 516547 567096 568346 569157 582716 583485 585101 586319 587941 638526 643935 686598 688383 690380 697951 699814 715244 717322 738621 755082 756240 757309 759409 790096 802189 867041 869394 872105 883267 885358 886729 887493 903071 903819 906730 947447 957206 974636 980413 981161 990544 1022494 1039396 1071415 1080798 1081546 1087323 1104034 1104753 1121398 1147038 1147817 1174466 1175230 1176601 1181406 1189854 1192565 1194918 1259770 1268850 1271863 1304650 1305695 1306877 1323338 1344637 1362145 1364008 1373576 1389760 1409048 1412041 1418024 1423433 1424101 1472458 1474830 1475640 1492802 1493613 1494863 1545412 1550516 1552384 1579663 1603817 1604377 1615021 1621687 1649710 1673594 1674556 1674980 1700088 1718002 1726698 1744772 1761104 1778773 1784873 1812784 1827845 1828284 1829842 1855816 1881122 1914412 1915850 2043948 
15.0 4.0 11.686 9.147 5.911 3.328 9.504 9.505 2.722 23.01 2.564 3.566 10.32 6.843 0.31 17.785 18.873 2.104 2.125 2.277 0.583 2.822 2.638 4.524 0.205 2.711 4.579 2.706 0.409 0.028 1.341 0.703 7.522 0.83 0.946 0.694 1.962 2.825 2.501 2.898 14.001 1.5 1.804 1.59 1.531 6.348 1.498 0.781 2.466 3.728 3.912 4.877 0.158 0.672 0.322 2.507 0.114 1.433 0.382 1.056 2.764 13.575 15.591 0.29 0.502 0.377 2.769 1.869 0.623 1.185 3.851 1.555 0.824 2.081 1.663 8.058 0.045 3.249 8.358 2.154 0.07 2.359 4.569 21.214 7.387 5.821 0.514 3.653 1.106 8.208 2.176 0.04 1.228 5.596 2.096 1.058 0.419 3.423 0.814 5.208 5.397 14.126 1.591 2.627 2.435 0.095 8.86 5.43 0.71 0.395 3.128 0.28 0.424 0.474 1.144 12.163 0.899 3.231 1.83 10.061 2.085 3.049 3.092 3.59 1.775 1.352 2.103 2.195 5.411 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:448
 Score: 107.60900000000001, AlignedPeaks: 756302 1039532 1176718 1305650 1475408 1603856 1717830 1880678 2043948 
0 100648 112769 130716 146855 232149 233763 276983 283218 300787 301297 344129 361687 387211 405216 456833 458105 511353 511859 566105 585234 585930 586551 589375 603314 613545 643882 692396 715264 715581 738000 754374 756302 759307 801928 820431 866528 869434 880586 882250 883490 885226 886260 887299 887684 902183 914110 941094 965621 974595 980655 983708 990585 990897 1022426 1039532 1087364 1096338 1104407 1121620 1147849 1174275 1176718 1178469 1179709 1180927 1181373 1181628 1192525 1195431 1241528 1259396 1260031 1305650 1307585 1316536 1323959 1346378 1363801 1386057 1408286 1409149 1412058 1418077 1423661 1423950 1434751 1444265 1448414 1458645 1472584 1474797 1475408 1476029 1476724 1492712 1493952 1495854 1542137 1550100 1550606 1597819 1603856 1621707 1649569 1656743 1674748 1692823 1700272 1717830 1744849 1760663 1761172 1778741 1784976 1812740 1828214 1829810 1855834 1880678 1915104 1931242 2043948 
15.0 4.572 12.025 9.398 5.081 3.741 8.291 0.182 2.697 21.214 20.208 3.845 7.712 1.512 0.324 0.509 16.897 2.687 0.917 1.695 9.422 5.589 5.362 0.121 3.071 1.547 1.41 1.015 2.752 2.832 3.435 4.334 16.278 0.605 1.902 1.885 1.149 1.557 0.024 3.433 2.238 9.43 1.567 3.421 3.965 1.503 0.152 1.492 0.987 2.953 1.691 2.779 1.868 2.499 9.134 11.14 0.564 2.309 1.052 0.248 1.538 2.21 5.728 2.051 2.732 4.763 8.553 8.553 2.955 3.083 0.172 1.449 3.827 24.474 3.214 0.332 14.405 0.481 3.025 0.806 2.989 0.293 1.362 6.472 1.037 1.005 0.449 1.974 0.88 4.9 0.274 1.957 5.622 4.903 9.522 1.092 4.987 5.053 0.034 3.221 2.441 5.746 3.395 0.891 2.023 4.488 5.813 0.474 0.973 9.379 1.24 4.512 1.755 9.905 1.826 1.839 3.098 3.358 0.759 1.593 2.412 5.228 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:445
 Score: 93.178, AlignedPeaks: 756309 1039448 1305544 1475449 1604070 1717663 1881210 2043845 
0 100685 113221 130615 147483 233792 277062 283212 299839 301107 317156 317609 327100 344192 360885 362247 387262 457799 480879 500076 503067 505339 511265 548269 568075 568868 569124 586101 586406 587208 643825 652724 705045 715133 733318 737945 744360 756309 790098 793200 802035 849804 872123 882347 885255 885527 887259 913432 932604 940605 949342 965620 974317 1000541 1022407 1039448 1061314 1081270 1087538 1104197 1104669 1121250 1129251 1147814 1174596 1180847 1181481 1189732 1212051 1259820 1260100 1271757 1305544 1317495 1323911 1346723 1361606 1386087 1389448 1409131 1412001 1418030 1423799 1434693 1444207 1472639 1474647 1475449 1475755 1492731 1492987 1493781 1513586 1550591 1556516 1558788 1561779 1575655 1592561 1598631 1603512 1604070 1662586 1674593 1699608 1700970 1717663 1734756 1744246 1744699 1760748 1778643 1784793 1812730 1828078 1829806 1855628 1881210 1914372 1915316 1931240 2043845 
15.0 4.672 12.19 8.782 6.168 7.984 0.739 1.97 1.014 19.856 2.762 4.175 0.121 1.972 1.589 4.93 0.002 13.058 2.395 0.982 0.076 0.606 2.48 3.877 7.505 2.641 2.547 4.257 6.692 0.101 0.713 0.033 2.161 2.075 0.077 3.778 0.744 15.084 0.443 1.422 1.096 0.162 0.335 1.016 2.051 0.313 4.138 2.763 5.715 0.027 0.033 0.161 2.095 5.849 3.157 5.612 6.69 0.335 0.535 1.471 1.823 0.58 2.573 1.678 1.504 1.872 3.141 0.904 0.435 2.476 3.427 4.113 24.916 0.726 9.668 2.486 0.069 1.472 0.045 0.063 1.083 5.91 1.7 1.72 1.529 0.37 2.337 4.792 1.273 9.003 10.759 13.466 1.115 3.109 2.784 0.05 2.977 0.491 2.36 5.697 4.015 4.016 0.999 3.263 0.281 0.838 7.01 0.982 4.247 4.249 2.034 8.405 2.053 2.989 2.714 1.132 0.972 1.748 2.237 2.496 4.501 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_625_0.prm:174
 Score: 75.969, AlignedPeaks: 902610 1039613 1168491 1225475 1466574 
0 159840 173848 208558 231104 275279 349400 374287 377812 412363 413148 442281 457350 487408 498020 510571 533658 570141 591696 617279 644312 656176 671360 696245 698432 699178 755402 766095 772537 774695 775391 783642 815321 824903 826596 844499 845299 851236 865807 875038 882042 884480 902610 909299 936300 938277 956606 967318 985624 1021314 1039202 1039613 1041882 1048886 1072653 1079425 1097328 1099021 1099682 1108603 1148533 1149229 1151387 1157829 1168491 1224746 1225475 1267748 1294427 1300573 1310567 1311229 1320082 1332228 1339659 1348508 1353783 1390266 1413353 1421776 1425904 1431088 1436516 1463805 1466574 1481643 1510778 1511561 1530106 1538588 1543003 1546112 1549534 1574524 1648544 1649806 1666693 1680648 1681815 1692820 1693768 1695635 1701777 1731614 1750076 1764084 1768622 1905914 
15.0 1.963 3.025 2.094 1.738 14.51 1.23 8.105 5.767 9.029 11.843 0.929 5.4 0.613 1.391 2.775 1.447 0.076 3.508 0.788 0.478 0.845 0.092 1.921 13.677 8.876 16.562 1.787 1.832 5.087 0.992 0.333 0.653 0.703 8.87 3.756 0.117 6.737 0.426 1.288 1.078 14.64 1.788 0.997 1.702 15.988 1.926 0.345 13.177 0.091 19.069 20.481 0.14 1.199 9.93 0.762 8.648 2.86 2.931 0.094 0.843 6.906 3.531 0.05 27.013 11.85 19.971 0.255 2.508 0.091 0.596 1.422 0.848 4.963 0.78 1.185 0.56 0.412 2.706 0.365 1.48 1.268 4.76 4.545 6.716 0.438 5.002 4.621 0.465 1.437 0.228 7.32 11.895 4.501 13.727 2.644 1.657 1.83 1.532 2.02 1.099 1.966 4.418 0.375 5.47 1.883 3.188 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:437
 Score: 72.128, AlignedPeaks: 676236 1096473 1225558 1282579 
0 174413 194161 212097 275053 287183 293657 374136 377717 378352 391937 442288 454284 483719 492663 493358 497819 510744 525168 530326 548388 603870 641193 641809 653598 656643 676236 696285 696946 698328 748884 753519 755360 756184 772619 773411 794502 826724 845343 852988 884438 894340 902815 903264 908401 919721 943317 944558 967463 985578 995333 1013478 1061220 1072473 1076980 1077677 1078126 1086601 1096473 1127953 1177472 1179507 1207530 1208322 1219682 1224757 1225558 1232057 1282579 1332428 1339748 1341159 1368104 1377071 1432555 1441647 1444388 1450615 1455773 1483122 1487583 1488278 1492021 1493620 1497222 1501201 1526657 1538653 1595846 1602589 1603224 1606882 1611581 1631563 1640043 1663708 1681799 1693758 1705944 1722737 1737735 1750777 1768849 1788680 1806528 1962931 
15.0 2.562 0.363 10.9 16.634 0.931 2.442 8.709 1.708 0.118 2.695 0.11 0.744 6.05 2.149 1.797 1.718 1.067 1.719 2.055 6.958 0.296 1.935 0.252 0.057 0.064 0.63 1.878 1.462 13.315 2.822 0.873 17.694 10.871 2.224 0.999 1.01 0.813 1.07 0.922 14.579 0.227 16.845 12.576 10.772 5.387 0.85 1.642 7.434 15.214 16.047 10.157 3.001 11.778 0.15 11.577 15.734 0.521 24.435 3.019 2.521 0.539 5.664 2.823 1.851 16.002 27.319 5.028 19.744 2.304 5.191 0.978 1.574 1.931 6.625 1.64 0.976 5.458 1.407 1.943 2.481 2.636 0.362 4.733 4.884 0.459 1.209 2.254 0.866 1.606 4.231 11.708 0.99 4.248 0.556 1.615 0.543 1.112 17.479 2.397 0.479 1.448 4.257 5.029 5.611 15.0 

SpectrumHMM Model: * M[0] - Mass:-756283.6666666666 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
 * M[1] - Mass:-455386.125 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:64.08000000000001, InsertsAfter: 24
 * M[2] - Mass:-298268.3333333333 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:48.827999999999996, InsertsAfter: 19
 * M[3] - Mass:0.0 Overlap:5/5 LogOddsScore:10.57419574607036, SumScore:90.726, InsertsAfter: 57
 * M[4] - Mass:128996.0 Overlap:3/5 LogOddsScore:2.0244298652718467, SumScore:15.209, InsertsAfter: 22
 * M[5] - Mass:266166.25 Overlap:3/5 LogOddsScore:3.2351722916053958, SumScore:25.866, InsertsAfter: 32
 * M[6] - Mass:283179.0 Overlap:5/5 LogOddsScore:8.152710893403263, SumScore:78.5145, InsertsAfter: 0
 * M[7] - Mass:420381.14285714284 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:41.086499999999994, InsertsAfter: 26
 * M[8] - Mass:549355.7777777778 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:135.906, InsertsAfter: 25
 * M[9] - Mass:605930.0 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:35.4795, InsertsAfter: 11
 * M[10] - Mass:718925.5555555555 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:50.755500000000005, InsertsAfter: 33
 * M[11] - Mass:847609.2222222221 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:54.4065, InsertsAfter: 30
 * M[12] - Mass:961570.6666666666 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:87.82800000000002, InsertsAfter: 18
 * M[13] - Mass:1124696.111111111 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:83.16600000000001, InsertsAfter: 29
 * M[14] - Mass:1287631.111111111 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:157.5, InsertsAfter: 7
 * M[15] - Mass:1400726.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:105.0, InsertsAfter: 0
ConsensusPRM: -756283 -455386 -298268 0 128996 266166 283179 420381 549355 605930 718925 847609 961570 1124696 1287631 1400726 Consensus: -756283 -455386 -298268 0 128996 266166 283179 420381 549355 605930 718925 847609 961570 1124696 1287631 1400726
De Novo: E[154.183]HEGIENYYI, Merged: E[154.183]HEGIENYYIKKTISRSPG
-756283 -455386 -298268 0 128996 266166 283179 420381 549355 605930 718925 847609 961570 1124696 1287631 1400726 1528820 1656914 1757961 1871045 1958077 2114178 2201210 2298262 2355283 
45.0 64.08000000000001 48.827999999999996 68.0445 15.209 25.866 62.343 37.39099999999999 100.604 33.653 43.837 46.271 73.552 80.44400000000002 135.0 105.0 105.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 

(LEFT)Round: 2 for seed: E[154.183]HEGIENYYIKKTISRSPG
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:448
 Score: 117.039, AlignedPeaks: 756302 885226 1039532 1176718 1305650 1475408 1603856 1717830 1880678 2043948 
0 100648 112769 130716 146855 232149 233763 276983 283218 300787 301297 344129 361687 387211 405216 456833 458105 511353 511859 566105 585234 585930 586551 589375 603314 613545 643882 692396 715264 715581 738000 754374 756302 759307 801928 820431 866528 869434 880586 882250 883490 885226 886260 887299 887684 902183 914110 941094 965621 974595 980655 983708 990585 990897 1022426 1039532 1087364 1096338 1104407 1121620 1147849 1174275 1176718 1178469 1179709 1180927 1181373 1181628 1192525 1195431 1241528 1259396 1260031 1305650 1307585 1316536 1323959 1346378 1363801 1386057 1408286 1409149 1412058 1418077 1423661 1423950 1434751 1444265 1448414 1458645 1472584 1474797 1475408 1476029 1476724 1492712 1493952 1495854 1542137 1550100 1550606 1597819 1603856 1621707 1649569 1656743 1674748 1692823 1700272 1717830 1744849 1760663 1761172 1778741 1784976 1812740 1828214 1829810 1855834 1880678 1915104 1931242 2043948 
15.0 4.572 12.025 9.398 5.081 3.741 8.291 0.182 2.697 21.214 20.208 3.845 7.712 1.512 0.324 0.509 16.897 2.687 0.917 1.695 9.422 5.589 5.362 0.121 3.071 1.547 1.41 1.015 2.752 2.832 3.435 4.334 16.278 0.605 1.902 1.885 1.149 1.557 0.024 3.433 2.238 9.43 1.567 3.421 3.965 1.503 0.152 1.492 0.987 2.953 1.691 2.779 1.868 2.499 9.134 11.14 0.564 2.309 1.052 0.248 1.538 2.21 5.728 2.051 2.732 4.763 8.553 8.553 2.955 3.083 0.172 1.449 3.827 24.474 3.214 0.332 14.405 0.481 3.025 0.806 2.989 0.293 1.362 6.472 1.037 1.005 0.449 1.974 0.88 4.9 0.274 1.957 5.622 4.903 9.522 1.092 4.987 5.053 0.034 3.221 2.441 5.746 3.395 0.891 2.023 4.488 5.813 0.474 0.973 9.379 1.24 4.512 1.755 9.905 1.826 1.839 3.098 3.358 0.759 1.593 2.412 5.228 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:449
 Score: 116.39899999999999, AlignedPeaks: 756240 885358 1039396 1176601 1305695 1362145 1474830 1603817 1718002 1881122 2043948 
0 101134 112687 130574 147547 232120 233674 234114 283186 300860 311423 317187 344051 361871 412249 457584 458142 482296 509575 511443 516547 567096 568346 569157 582716 583485 585101 586319 587941 638526 643935 686598 688383 690380 697951 699814 715244 717322 738621 755082 756240 757309 759409 790096 802189 867041 869394 872105 883267 885358 886729 887493 903071 903819 906730 947447 957206 974636 980413 981161 990544 1022494 1039396 1071415 1080798 1081546 1087323 1104034 1104753 1121398 1147038 1147817 1174466 1175230 1176601 1181406 1189854 1192565 1194918 1259770 1268850 1271863 1304650 1305695 1306877 1323338 1344637 1362145 1364008 1373576 1389760 1409048 1412041 1418024 1423433 1424101 1472458 1474830 1475640 1492802 1493613 1494863 1545412 1550516 1552384 1579663 1603817 1604377 1615021 1621687 1649710 1673594 1674556 1674980 1700088 1718002 1726698 1744772 1761104 1778773 1784873 1812784 1827845 1828284 1829842 1855816 1881122 1914412 1915850 2043948 
15.0 4.0 11.686 9.147 5.911 3.328 9.504 9.505 2.722 23.01 2.564 3.566 10.32 6.843 0.31 17.785 18.873 2.104 2.125 2.277 0.583 2.822 2.638 4.524 0.205 2.711 4.579 2.706 0.409 0.028 1.341 0.703 7.522 0.83 0.946 0.694 1.962 2.825 2.501 2.898 14.001 1.5 1.804 1.59 1.531 6.348 1.498 0.781 2.466 3.728 3.912 4.877 0.158 0.672 0.322 2.507 0.114 1.433 0.382 1.056 2.764 13.575 15.591 0.29 0.502 0.377 2.769 1.869 0.623 1.185 3.851 1.555 0.824 2.081 1.663 8.058 0.045 3.249 8.358 2.154 0.07 2.359 4.569 21.214 7.387 5.821 0.514 3.653 1.106 8.208 2.176 0.04 1.228 5.596 2.096 1.058 0.419 3.423 0.814 5.208 5.397 14.126 1.591 2.627 2.435 0.095 8.86 5.43 0.71 0.395 3.128 0.28 0.424 0.474 1.144 12.163 0.899 3.231 1.83 10.061 2.085 3.049 3.092 3.59 1.775 1.352 2.103 2.195 5.411 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_675_0.prm:445
 Score: 95.229, AlignedPeaks: 756309 885255 1039448 1305544 1475449 1604070 1717663 1881210 2043845 
0 100685 113221 130615 147483 233792 277062 283212 299839 301107 317156 317609 327100 344192 360885 362247 387262 457799 480879 500076 503067 505339 511265 548269 568075 568868 569124 586101 586406 587208 643825 652724 705045 715133 733318 737945 744360 756309 790098 793200 802035 849804 872123 882347 885255 885527 887259 913432 932604 940605 949342 965620 974317 1000541 1022407 1039448 1061314 1081270 1087538 1104197 1104669 1121250 1129251 1147814 1174596 1180847 1181481 1189732 1212051 1259820 1260100 1271757 1305544 1317495 1323911 1346723 1361606 1386087 1389448 1409131 1412001 1418030 1423799 1434693 1444207 1472639 1474647 1475449 1475755 1492731 1492987 1493781 1513586 1550591 1556516 1558788 1561779 1575655 1592561 1598631 1603512 1604070 1662586 1674593 1699608 1700970 1717663 1734756 1744246 1744699 1760748 1778643 1784793 1812730 1828078 1829806 1855628 1881210 1914372 1915316 1931240 2043845 
15.0 4.672 12.19 8.782 6.168 7.984 0.739 1.97 1.014 19.856 2.762 4.175 0.121 1.972 1.589 4.93 0.002 13.058 2.395 0.982 0.076 0.606 2.48 3.877 7.505 2.641 2.547 4.257 6.692 0.101 0.713 0.033 2.161 2.075 0.077 3.778 0.744 15.084 0.443 1.422 1.096 0.162 0.335 1.016 2.051 0.313 4.138 2.763 5.715 0.027 0.033 0.161 2.095 5.849 3.157 5.612 6.69 0.335 0.535 1.471 1.823 0.58 2.573 1.678 1.504 1.872 3.141 0.904 0.435 2.476 3.427 4.113 24.916 0.726 9.668 2.486 0.069 1.472 0.045 0.063 1.083 5.91 1.7 1.72 1.529 0.37 2.337 4.792 1.273 9.003 10.759 13.466 1.115 3.109 2.784 0.05 2.977 0.491 2.36 5.697 4.015 4.016 0.999 3.263 0.281 0.838 7.01 0.982 4.247 4.249 2.034 8.405 2.053 2.989 2.714 1.132 0.972 1.748 2.237 2.496 4.501 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_850_0.prm:509
 Score: 71.404, AlignedPeaks: 921437 1187565 1244375 1485607 1763039 1925600 
0 203993 238701 260115 274912 289190 310108 332554 349611 350262 364259 366891 368465 372416 461100 473657 479258 483020 517212 538101 551706 561899 575867 594228 600246 608328 622399 665911 681501 710118 722197 725032 733809 734554 735286 742956 777517 786386 794807 838444 842787 844062 850639 851517 857197 858727 920361 921437 933646 935932 939462 942621 992218 999364 1004765 1034515 1052389 1055319 1063927 1064527 1069221 1085430 1108519 1119318 1121447 1128745 1137335 1139678 1157598 1184200 1187565 1192878 1196554 1202194 1218264 1226166 1236516 1244375 1254379 1275441 1282302 1324799 1331590 1349705 1362690 1370585 1380935 1388837 1404907 1410547 1414223 1419475 1422901 1467423 1478356 1485607 1487783 1503693 1537880 1542574 1543174 1551782 1554712 1572556 1606775 1607737 1614883 1649593 1664480 1667639 1668369 1671169 1673455 1685664 1686740 1748374 1749904 1755584 1756462 1763039 1764314 1768657 1812294 1820715 1829584 1862858 1864145 1871815 1872547 1873292 1882069 1884904 1896983 1925600 1941190 1984702 1998773 2000652 2006855 2012873 2031234 2045202 2046161 2055395 2060389 2089888 2102812 2124081 2127851 2133444 2146001 2170907 2202942 2220948 2234685 2238636 2240210 2256839 2290804 2296993 2332189 2346986 2403108 2404388 2452332 2589091 
15.0 3.418 0.702 2.145 3.428 2.096 2.678 2.412 0.913 15.135 4.916 4.63 7.735 2.023 1.399 1.941 11.871 2.162 0.892 4.174 2.278 1.938 2.041 4.222 2.668 7.783 7.098 2.58 2.885 2.903 9.553 1.827 1.588 6.502 6.612 5.097 2.765 2.169 2.732 3.883 3.731 2.226 3.061 2.152 4.011 1.972 1.202 7.77 1.937 3.156 3.462 1.255 2.482 1.233 0.707 16.166 8.501 1.029 1.668 2.402 1.692 0.906 1.05 5.477 27.144 2.226 3.846 12.68 4.285 1.869 11.38 2.492 2.67 1.068 5.418 2.115 2.317 15.199 0.741 10.44 0.863 0.865 8.119 2.986 14.633 3.083 5.847 4.994 2.554 2.684 2.276 11.882 1.365 7.655 0.548 31.049 7.109 11.427 1.484 3.466 1.651 2.282 6.055 24.135 3.098 1.896 2.147 1.573 3.047 4.258 0.172 3.011 1.4 13.544 1.037 1.94 5.931 3.06 3.128 2.513 3.332 3.702 3.307 3.844 2.977 7.024 6.506 10.873 10.336 7.352 3.206 11.632 3.244 3.493 3.823 6.738 7.105 1.079 3.321 2.904 1.06 0.241 6.489 1.655 0.295 6.458 1.093 0.9 12.394 0.556 1.833 0.498 1.12 1.008 0.096 1.237 5.073 12.66 1.325 0.089 1.705 0.771 5.48 7.641 2.282 15.0 

SpectrumHMM Model: * M[0] - Mass:-756283.6666666666 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
 * M[1] - Mass:-455386.125 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:64.08000000000001, InsertsAfter: 24
 * M[2] - Mass:-298268.3333333333 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:48.827999999999996, InsertsAfter: 19
 * M[3] - Mass:0.0 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:113.4075, InsertsAfter: 57
 * M[4] - Mass:129001.55555555555 Overlap:5/5 LogOddsScore:4.520483614402617, SumScore:30.418, InsertsAfter: 22
 * M[5] - Mass:266166.25 Overlap:3/5 LogOddsScore:3.2351722916053958, SumScore:25.866, InsertsAfter: 32
 * M[6] - Mass:283179.44444444444 Overlap:5/5 LogOddsScore:8.658986165564308, SumScore:94.68599999999999, InsertsAfter: 0
 * M[7] - Mass:420387.4285714286 Overlap:4/5 LogOddsScore:5.69394159250433, SumScore:44.78199999999999, InsertsAfter: 26
 * M[8] - Mass:549359.3333333334 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:171.208, InsertsAfter: 25
 * M[9] - Mass:605911.25 Overlap:3/5 LogOddsScore:4.445914717938945, SumScore:37.306, InsertsAfter: 11
 * M[10] - Mass:718921.4444444445 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:57.67400000000001, InsertsAfter: 33
 * M[11] - Mass:847613.7777777778 Overlap:5/5 LogOddsScore:6.941968467069715, SumScore:62.542, InsertsAfter: 30
 * M[12] - Mass:961572.0 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:102.10400000000001, InsertsAfter: 18
 * M[13] - Mass:1124696.888888889 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:85.88800000000002, InsertsAfter: 29
 * M[14] - Mass:1287640.5555555555 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:180.0, InsertsAfter: 7
ConsensusPRM: -756283 -455386 -298268 0 129001 266166 283179 420387 549359 605911 718921 847613 961572 1124696 1287640 Consensus: -756283 -455386 -298268 0 129001 266166 283179 420387 549359 605911 718921 847613 961572 1124696 1287640
De Novo: E[154.178]HEGIENYY, Merged: E[154.178]HEGIENYYIKKTISRSPG
-756283 -455386 -298268 0 129001 266166 283179 420387 549359 605911 718921 847613 961572 1124696 1287640 1400735 1528829 1656923 1757970 1871054 1958086 2114187 2201219 2298271 2355292 
45.0 64.08000000000001 48.827999999999996 90.726 22.813499999999998 25.866 78.5145 41.08649999999999 135.906 35.4795 50.755500000000005 54.4065 87.828 83.16600000000003 157.5 105.0 105.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 
(RIGHT)Round: 0 for seed: E[154.183]HEGIENYYIKKTISRSPG
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_975_0.prm:15
 Score: 131.33100000000002, AlignedPeaks: 969160 1097419 1225534 1326665 1439669 1526214 1866824 
0 259235 275673 278325 281441 284907 286166 287067 295271 310931 325218 344933 345758 346427 364013 368203 385916 407143 449184 458467 459313 511462 513188 517958 521173 558286 612817 613439 663598 669340 672276 710877 719300 719934 745268 754150 762475 794874 803923 812527 860380 861042 869233 869914 883420 911635 924512 933176 967607 969160 970158 974055 976309 1079534 1091159 1096404 1097419 1100998 1101731 1115327 1115930 1124390 1136929 1137597 1142558 1166660 1208474 1212715 1221544 1225534 1242441 1243424 1244004 1252897 1289175 1300124 1308909 1309664 1312302 1325564 1326665 1337321 1338596 1339677 1352513 1356588 1362963 1400195 1409245 1438047 1439669 1441269 1446047 1455200 1455851 1480583 1483678 1508410 1509061 1522992 1524547 1526214 1526701 1555016 1564066 1601298 1607673 1611748 1619967 1624584 1625666 1626940 1628421 1637596 1638697 1651959 1654597 1655352 1664137 1675086 1711364 1720257 1720837 1721820 1738730 1751546 1755787 1797601 1821703 1826664 1827332 1839871 1848331 1848934 1862530 1863263 1866824 1867857 1873102 1884727 1911923 1976399 1987952 1990206 1994103 1995101 1996654 2031085 2039749 2048908 2052626 2080841 2094347 2095027 2103219 2103881 2151734 2160338 2169387 2201786 2210111 2218993 2244327 2244961 2253384 2291985 2294921 2300663 2350822 2351444 2360389 2405975 2415406 2424234 2432989 2446302 2451072 2452799 2504948 2505794 2515077 2578349 2596058 2617824 2618503 2639043 2653330 2668990 2677194 2678095 2679354 2682820 2685936 2688588 2705026 2818490 2946251 
15.0 2.701 2.567 0.228 1.006 0.94 6.72 3.915 3.293 1.189 0.492 2.19 7.474 9.096 4.904 1.136 13.359 0.956 0.213 3.731 10.202 8.01 4.627 0.482 1.245 2.833 0.792 1.105 2.194 3.993 2.403 3.229 2.401 2.867 2.184 3.314 7.495 1.113 3.247 4.428 6.066 2.793 2.479 2.593 1.993 3.048 3.254 1.882 2.751 2.359 2.64 2.727 1.963 4.7 2.877 4.867 27.403 1.266 1.053 15.116 12.702 2.225 3.33 2.975 1.427 1.926 4.583 1.78 1.958 25.468 3.952 13.16 17.788 1.895 1.226 3.147 3.163 0.635 2.198 2.005 6.22 1.892 16.2 9.835 3.195 14.882 4.145 2.172 1.622 10.623 17.735 0.703 0.694 9.838 6.111 4.379 5.82 3.642 7.078 1.133 16.878 15.399 6.71 1.967 0.814 2.333 9.321 2.903 5.659 11.489 28.128 2.607 1.16 4.428 1.8 0.964 0.45 2.897 3.419 0.84 2.084 5.392 5.349 6.118 29.197 1.821 6.045 1.883 2.61 1.623 3.832 1.536 11.378 3.759 1.289 1.175 36.747 6.84 0.818 13.109 2.926 1.148 2.3 2.987 2.569 1.741 2.481 4.296 5.531 0.662 2.924 3.463 3.319 4.136 3.008 6.266 2.661 7.384 3.744 6.58 3.631 3.915 4.608 2.919 3.445 4.698 3.678 0.579 2.954 5.927 4.534 0.53 7.309 3.014 2.059 0.639 1.113 6.318 10.225 0.08 0.208 9.659 1.697 9.849 5.159 1.243 0.055 1.142 1.904 6.124 1.222 1.35 0.024 3.787 4.09 3.824 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_400_0.prm:622
 Score: 121.336, AlignedPeaks: 0 128350 229403 342502 585393 672413 826726 
0 128350 172273 229403 276091 276522 342502 431296 440576 468829 482823 516191 516777 543392 551550 568214 568646 585393 615308 672413 698359 725888 826726 
15.0 17.989 10.096 23.519 1.871 1.872 5.323 4.657 5.787 0.202 0.523 1.271 1.753 0.202 4.901 7.218 7.559 1.11 5.846 13.395 16.19 2.226 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_400_0.prm:624
 Score: 114.508, AlignedPeaks: 0 128152 229151 342202 585398 672271 826457 
0 128152 172240 229151 276151 316419 342202 422632 430630 431277 440271 458478 468320 480498 550515 568328 585398 615327 672271 698414 826457 
15.0 17.932 0.207 22.577 2.948 0.553 4.597 3.303 3.272 3.636 4.39 1.284 1.339 1.352 1.949 8.159 1.821 16.106 7.581 16.04 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:673
 Score: 112.98400000000001, AlignedPeaks: 0 241246 369494 470402 826562 913658 1067744 
0 172096 173690 241246 259160 369494 387223 442683 456038 470402 471152 552193 559181 560606 565949 588260 589266 621012 638569 641297 663465 672061 675538 716298 730261 734406 735164 751664 752323 767829 784434 826562 912064 913658 1067744 
15.0 1.663 3.951 18.083 7.599 15.176 0.354 2.986 2.874 3.101 1.343 3.912 2.413 4.091 1.93 3.253 1.158 1.29 3.28 1.904 3.641 2.202 4.528 10.291 0.726 3.04 0.996 1.725 3.79 0.701 0.243 13.629 7.629 2.995 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_400_0.prm:512
 Score: 112.29100000000001, AlignedPeaks: 163026 276027 404403 532263 633419 746480 1076800 1230722 
0 128227 163026 172062 184230 196114 214129 244228 266348 276027 294401 298783 300293 302498 307742 335294 398130 403933 404403 404715 422143 422441 440481 448094 448360 465150 502252 522174 529112 529573 532263 533466 550323 564372 570879 576490 593357 615310 633419 698409 715266 716444 719159 726558 746480 762374 771289 800372 800638 808251 826291 826589 838546 844017 844343 844799 847729 850602 875482 889434 899478 913438 954331 972713 982384 992495 1000559 1034603 1062515 1076800 1102551 1230722 
15.0 0.913 11.782 6.041 4.324 0.11 2.58 2.553 0.443 19.642 4.394 0.483 0.245 0.772 5.499 1.839 0.472 2.735 8.604 9.814 2.534 1.07 6.51 1.091 1.646 0.729 4.542 0.583 1.127 4.926 6.569 0.407 10.378 0.585 0.894 1.165 0.709 15.379 21.077 3.864 3.545 25.604 3.281 0.597 6.075 1.206 0.079 1.132 0.192 0.903 1.202 4.513 1.177 12.699 11.978 10.577 0.805 0.349 3.445 0.522 3.964 0.184 0.43 10.413 1.631 2.488 5.211 4.1 3.498 8.542 4.225 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:4/4 LogOddsScore:7.754889442683784, SumScore:161.782, InsertsAfter: 15
 * M[1] - Mass:113063.66666666667 Overlap:4/5 LogOddsScore:7.410959290998923, SumScore:127.00099999999999, InsertsAfter: 16
 * M[2] - Mass:241257.33333333334 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:189.08999999999997, InsertsAfter: 24
 * M[3] - Mass:369393.8333333333 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:158.134, InsertsAfter: 22
 * M[4] - Mass:470442.8333333333 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:151.494, InsertsAfter: 23
 * M[5] - Mass:583510.8 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:108.72999999999999, InsertsAfter: 24
 * M[6] - Mass:670297.5 Overlap:3/7 LogOddsScore:5.475072113063814, SumScore:90.399, InsertsAfter: 59
 * M[7] - Mass:826569.5 Overlap:5/7 LogOddsScore:7.971125862194585, SumScore:91.56, InsertsAfter: 14
 * M[8] - Mass:913614.6000000001 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:107.513, InsertsAfter: 13
 * M[9] - Mass:1010695.0 Overlap:3/7 LogOddsScore:5.7282097491443364, SumScore:111.747, InsertsAfter: 4
 * M[10] - Mass:1067730.6 Overlap:6/7 LogOddsScore:12.851380015760617, SumScore:135.0, InsertsAfter: 56
ConsensusPRM: 0 113063 241257 369393 470442 583510 670297 826569 913614 1010695 1067730 Consensus: 0 113063 241257 369393 470442 583510 670297 826569 913614 1010695 1067730
De Novo: IKKTISRSPG, Merged: E[154.183]HEGIENYYIKKTISRSPG
0 128996 283179 420381 549355 605930 718925 847609 961570 1124696 1287631 1400726 1528820 1656914 1757961 1871045 1958077 2114178 2201210 2298262 2355283 
68.0445 15.209 62.343 37.39099999999999 100.604 33.653 43.837 46.271 73.552 80.44400000000002 148.39100000000002 114.3320668729493 147.045 116.567 113.247 90.19656687294929 76.02576749179718 79.94313374589859 89.5880668729493 86.69976749179719 103.3315668729493 

(LEFT)Round: 0 for seed: DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSY
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_900_0.prm:150
 Score: 97.15499999999999, AlignedPeaks: 239818 339048 469990 557143 685097 772192 869235 956199 1043270 
0 239818 275567 332200 339048 349979 350603 355921 372234 431252 441226 469990 488060 518207 530131 536110 554266 557143 572106 617293 685097 688238 706293 772192 801379 810302 811012 856955 869235 888422 904347 905017 908476 913421 939573 940243 956199 987635 1043270 1043826 1050448 1072441 1091531 1100536 1108848 1156307 1159471 1227321 1270387 1287490 1314459 1326383 1374617 1411541 1413445 1494611 1498209 1505521 1512448 1533701 1542426 1569023 1569664 1596325 1698659 1826580 
15.0 2.481 3.078 13.947 19.043 9.861 5.521 2.514 2.944 9.062 0.217 11.166 0.254 14.435 0.714 8.368 0.322 12.466 1.595 7.73 13.125 6.01 3.722 19.223 9.705 1.238 0.574 1.232 3.237 5.144 1.6 1.303 0.181 1.187 4.939 2.875 5.922 0.049 10.492 5.903 0.132 11.852 5.477 2.513 0.171 13.798 5.288 12.157 0.565 9.591 0.437 18.81 7.661 0.418 13.308 0.957 0.413 18.973 24.387 1.313 0.188 2.862 7.927 1.14 10.048 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1050_0.prm:60
 Score: 95.88699999999999, AlignedPeaks: 1564488 1663615 1794726 1881734 2009770 2096699 2280593 2367895 
0 158030 193788 205884 274579 302132 316186 328100 329309 331780 332220 336173 346115 349683 366586 368014 371386 415166 420292 430740 431299 432952 449105 461943 500331 502095 516940 518258 532372 535688 553574 586110 594212 597199 615365 617174 635190 669941 673286 687352 688254 705886 725708 744174 752976 768570 778161 782397 793516 801340 831924 879620 888600 897429 923062 930467 931744 940960 996005 1004801 1005410 1030482 1038888 1039547 1040181 1041758 1044785 1072493 1140472 1142769 1159423 1174954 1195494 1206135 1231653 1240536 1267019 1275999 1286517 1287478 1296185 1298783 1307809 1316752 1320371 1356400 1369226 1369684 1373417 1374458 1400589 1401303 1409755 1418712 1438175 1447307 1459108 1461432 1481654 1484317 1487702 1503673 1505579 1511835 1522132 1534790 1563556 1564488 1582405 1586788 1604731 1605637 1634403 1647061 1657358 1658161 1663615 1665520 1681491 1684876 1687539 1707761 1710085 1721886 1731018 1750487 1759438 1761052 1767890 1768604 1794726 1795776 1799509 1799967 1812793 1843067 1843731 1848822 1852441 1854472 1861384 1870410 1873008 1873807 1881734 1882676 1893194 1902174 1928657 1937540 1962433 1973699 1979134 1994239 1996972 2009770 2026424 2028721 2096699 2124408 2127435 2129012 2129646 2130304 2133014 2138711 2163783 2164392 2173188 2228233 2237449 2238726 2246131 2271764 2280593 2289573 2294127 2303741 2337269 2367895 2375677 2386796 2391032 2400623 2416217 2425019 2426769 2443485 2481011 2481841 2495907 2499252 2534027 2552006 2553828 2571331 2583083 2633504 2636821 2650928 2707250 2720088 2736241 2737894 2754027 2797807 2819510 2823078 2833020 2836973 2837412 2853007 2867061 2894614 2963308 3151182 
15.0 2.803 2.24 1.544 2.932 2.983 3.501 0.948 1.357 13.331 13.33 2.231 4.352 6.76 1.674 5.994 2.794 0.269 1.969 3.331 9.329 1.891 3.729 2.807 0.181 0.112 2.085 16.528 0.47 3.011 1.833 0.357 1.667 0.572 6.628 9.166 11.28 3.218 6.586 11.706 14.244 8.275 1.795 5.437 3.102 1.715 7.005 1.977 2.091 6.225 2.116 2.732 5.903 3.897 2.872 2.432 3.449 2.837 1.139 2.575 2.832 2.812 2.269 3.289 0.817 2.308 2.033 3.169 3.115 3.895 12.535 3.321 0.403 0.5 2.903 2.153 0.851 1.408 6.052 14.509 1.448 1.239 3.199 0.995 0.009 2.652 5.35 3.712 6.524 18.303 0.76 1.436 2.458 6.485 6.035 1.306 1.457 2.357 2.453 4.654 3.001 0.905 24.466 2.406 1.777 1.8 2.837 10.367 9.651 3.272 18.23 0.039 0.161 2.13 2.614 0.147 17.61 3.594 11.318 6.231 2.732 2.545 2.02 1.386 6.041 7.218 4.317 1.825 3.994 2.868 19.626 1.658 6.191 6.191 14.929 0.668 2.813 0.027 0.613 0.205 3.758 0.799 0.756 0.948 10.609 2.202 1.125 2.704 4.301 5.896 0.62 1.755 2.963 3.505 1.437 14.306 6.076 3.322 6.469 3.025 1.68 3.068 2.696 6.052 10.891 4.151 5.843 8.33 2.363 3.697 3.751 3.847 4.348 7.334 6.785 1.745 2.582 6.213 10.036 10.115 3.073 3.632 5.957 1.934 4.794 5.525 5.838 3.278 16.959 6.351 1.764 1.024 2.22 11.147 6.148 0.064 0.275 0.119 1.37 19.373 0.727 0.176 2.699 6.891 0.08 0.055 0.686 4.131 0.452 15.527 14.727 1.195 1.957 3.029 1.998 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_825_0.prm:572
 Score: 78.425, AlignedPeaks: 934121 1033403 1164238 1251599 1379582 1466480 
0 199789 210563 220165 275316 276997 292905 297873 312850 315248 332009 341980 343337 346207 348835 350127 394001 408063 418142 431366 433146 445326 453663 462422 472125 503039 518167 519208 536117 536731 579868 617509 634891 643875 667816 678564 680921 687582 688326 689693 715402 724638 733481 746956 772815 793604 802580 816946 828871 832660 834306 834963 873851 916223 934121 946631 951938 960857 965706 991997 1001415 1010497 1033403 1038454 1045073 1049450 1053836 1065438 1072466 1075582 1090480 1094406 1095052 1115786 1123017 1124158 1159377 1159916 1164238 1169575 1183693 1187290 1196362 1203307 1216037 1222415 1238313 1250934 1251599 1252319 1268510 1270402 1286620 1287355 1288005 1316524 1322902 1342577 1351649 1355246 1369364 1374636 1379023 1379582 1415922 1423153 1435383 1443887 1444533 1448459 1463357 1466480 1473501 1485103 1493866 1500484 1505547 1528442 1537524 1573233 1578082 1587001 1592308 1604818 1622716 1665088 1703976 1704633 1706279 1710043 1721993 1736359 1745335 1766124 1791983 1805458 1814301 1823537 1849246 1850613 1851357 1858018 1860375 1895064 1904048 1921430 1959071 2002208 2002827 2019730 2020896 2035900 2069751 2076516 2093612 2105793 2107626 2120797 2188812 2190104 2192732 2207041 2223691 2226089 2246034 2261942 2263623 2318774 2392724 2520929 
15.0 2.657 2.634 4.556 2.236 2.951 3.299 1.628 1.991 2.786 12.208 1.374 3.027 0.45 0.31 5.845 5.939 0.849 2.519 5.594 1.336 2.639 0.178 3.873 3.146 4.398 7.773 3.607 15.302 15.026 1.635 8.507 8.115 3.275 1.898 1.992 6.781 2.297 2.982 1.738 1.412 2.307 5.575 2.045 1.423 1.365 2.185 1.976 4.463 2.312 2.898 3.854 6.348 2.13 9.084 2.337 8.661 2.58 2.109 0.202 1.687 2.846 3.73 3.755 2.014 0.811 7.537 0.559 15.41 1.763 7.447 1.616 1.425 1.678 0.598 0.596 14.291 9.59 9.195 0.114 0.165 5.016 2.07 0.861 2.483 2.411 2.233 6.243 14.907 3.803 12.426 10.021 2.635 15.05 6.308 0.348 1.535 1.294 2.177 0.431 1.784 10.446 10.739 17.978 1.082 1.954 1.856 1.886 2.226 7.713 0.668 23.531 0.586 3.968 3.162 6.253 5.098 4.321 2.667 1.911 3.508 5.758 1.391 9.337 5.047 4.455 5.297 3.492 1.174 8.866 1.088 2.726 1.859 0.936 2.827 5.595 3.834 3.441 6.008 5.628 7.151 2.365 2.472 2.381 8.138 11.109 3.187 4.566 7.625 1.314 16.073 1.672 0.149 1.743 1.696 1.514 9.738 0.555 0.971 0.216 1.449 16.163 0.301 0.491 0.154 1.871 3.111 3.489 4.933 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/5 LogOddsScore:3.704163115534604, SumScore:1185.0, InsertsAfter: 126
 * M[1] - Mass:115026.0 Overlap:2/5 LogOddsScore:3.704163115534604, SumScore:1230.0, InsertsAfter: 19
 * M[2] - Mass:228110.0 Overlap:5/5 LogOddsScore:7.448243739230759, SumScore:1251.932, InsertsAfter: 17
 * M[3] - Mass:327286.75 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:1270.3829999999998, InsertsAfter: 17
 * M[4] - Mass:458268.75 Overlap:5/5 LogOddsScore:8.658986165564308, SumScore:1449.9869999999999, InsertsAfter: 34
 * M[5] - Mass:545407.25 Overlap:5/5 LogOddsScore:8.658986165564308, SumScore:1507.9819999999997, InsertsAfter: 27
 * M[6] - Mass:673415.0 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:1560.409, InsertsAfter: 26
 * M[7] - Mass:760403.5 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:1564.223, InsertsAfter: 11
 * M[8] - Mass:857459.5 Overlap:3/5 LogOddsScore:4.952189990099989, SumScore:1518.237, InsertsAfter: 21
 * M[9] - Mass:944376.6666666667 Overlap:4/5 LogOddsScore:6.200216864665374, SumScore:1542.707, InsertsAfter: 18
 * M[10] - Mass:1031511.6666666666 Overlap:4/4 LogOddsScore:6.5441470163502355, SumScore:1565.607, InsertsAfter: 12
ConsensusPRM: 0 115026 228110 327286 458268 545407 673415 760403 857459 944376 1031511 Consensus: 0 115026 228110 327286 458268 545407 673415 760403 857459 944376 1031511
De Novo: DIVMSQSPSS, Merged: DIVMSQSPSSIAVSVGEKVTMSCKSSQSIIYSSNQKNYIAWYQQKPGQSPKIIIYWASTRESGVPDRFTGSGSGTDFTITISSVKAEDIAVYYCQQYYSY
0 115026 228110 327286 458268 545407 673415 760403 857459 944376 1031511 1144595 1215632 1314700 1401732 1500800 1557821 1686863 1814957 1914025 2015072 2146112 2233144 2393228 2521322 2608354 2695386 2823444 2910476 3023560 3136644 3299707 3386739 3473771 3587813 3715871 3843965 3958007 4121070 4234154 4305191 4491270 4654333 4782391 4910449 5038543 5135595 5192616 5320674 5407706 5504758 5632852 5745936 5859020 5972104 6135167 6321246 6392283 6479315 6580362 6736463 6865505 6952537 7009558 7108626 7205678 7320704 7476805 7623873 7724920 7781941 7868973 7925994 8013026 8070047 8171094 8286120 8433188 8534235 8647319 8748366 8861450 8948482 9035514 9134582 9262676 9333713 9462755 9577781 9690865 9761902 9860970 10024033 10187096 10347180 10475238 10603296 10766359 10929422 11016454 11179517 
1185.0 1230.0 1240.966 1250.1915 1429.9935 1488.991 1537.7045 1539.6115 1516.6185 1536.3535000000002 1555.3035 1740.0 1680.0 1590.0 1575.0 1575.0 1575.0 1590.0 1275.0 495.0 480.0 570.0 210.0 255.0 300.0 300.0 300.0 300.0 300.0 300.0 270.0 180.0 120.0 120.0 165.0 150.0 165.0 135.0 195.0 255.0 255.0 360.0 360.0 360.0 375.0 435.0 435.0 435.0 435.0 435.0 465.0 945.0 795.0 885.0 810.0 795.0 795.0 780.0 780.0 795.0 780.0 45.0 45.0 45.0 45.0 45.0 45.0 375.0 375.0 390.0 390.0 390.0 390.0 390.0 390.0 390.0 465.0 525.0 525.0 555.0 555.0 540.0 540.0 540.0 540.0 555.0 225.0 225.0 180.0 150.0 60.0 60.0 45.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 
(RIGHT)Round: 0 for seed: DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSY
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1075_0.prm:30
 Score: 169.981, AlignedPeaks: 499082 598130 761170 924251 1212327 1340353 1503409 1666468 1753514 1916672 
0 201873 208534 271043 271605 287083 287721 289188 299172 305165 308989 315270 316773 395159 398270 402245 427899 433468 434213 436251 452194 467134 478170 497948 499082 521253 553234 570179 598130 598545 614058 630008 662269 683852 684309 721286 733300 760498 761170 793142 825043 847370 870303 896253 899551 900326 924251 934833 936289 941229 974511 975376 1001475 1031650 1066269 1073239 1075833 1076148 1080484 1082081 1084968 1085515 1102747 1105634 1111567 1114476 1121446 1194276 1212327 1246438 1251426 1263452 1340353 1392855 1404480 1409524 1425516 1426545 1454415 1466429 1471548 1503409 1503863 1525446 1573657 1589596 1617536 1626513 1634481 1666468 1678686 1688673 1689767 1753514 1759816 1789444 1870942 1872444 1878725 1881635 1882607 1888543 1897815 1898527 1899994 1900632 1916110 1916672 1979181 1985842 2169704 
15.0 1.989 0.781 14.01 7.252 4.106 2.994 8.456 4.192 13.881 1.559 7.376 1.114 1.972 0.217 2.986 6.127 2.605 9.515 1.178 4.907 2.154 0.107 2.623 10.573 13.917 0.392 1.608 24.031 4.447 0.407 1.06 0.151 14.023 15.973 0.184 1.249 9.124 19.599 0.411 1.085 11.849 0.788 0.479 0.627 0.373 18.18 0.885 0.12 5.268 2.084 11.702 1.325 5.93 0.588 0.804 0.743 0.676 1.548 0.462 1.624 1.561 0.918 0.396 2.169 0.273 1.864 0.115 16.515 2.259 0.177 14.009 15.298 1.322 1.094 0.462 1.411 10.721 1.615 0.523 0.279 17.654 0.118 1.61 2.518 12.724 1.574 0.025 0.936 14.881 0.126 5.933 0.143 16.832 0.643 0.035 0.028 2.069 0.595 0.276 3.911 2.555 1.341 11.394 14.231 5.091 10.812 16.418 0.069 1.529 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_1075_0.prm:10
 Score: 167.308, AlignedPeaks: 499086 598152 761155 924203 1212243 1340351 1503385 1666469 1753502 1916567 
0 271152 286342 287124 289206 299043 307399 309288 315090 315699 317633 321460 339098 381298 398119 428135 434230 452251 467021 469241 499086 521227 538471 553402 570265 598152 615096 615862 630161 632220 684313 761155 778301 794881 847308 879937 924203 935482 939900 941747 946428 953051 974121 974913 975400 985184 993560 1039303 1066172 1068344 1076556 1078653 1085185 1102533 1121546 1194081 1202534 1212243 1212806 1251257 1263474 1339241 1340351 1343496 1362217 1392838 1409417 1412602 1426552 1466984 1471402 1503385 1525603 1555499 1557557 1589588 1634317 1648453 1649248 1665492 1666469 1678500 1688703 1753502 1759543 1773626 1789599 1848620 1866258 1872628 1878430 1880319 1881478 1882092 1888676 1898512 1900594 1901376 1916567 2169708 
15.0 12.367 1.341 3.557 8.35 5.018 0.745 2.983 6.894 6.716 1.204 3.673 13.24 0.847 0.77 11.448 7.406 6.869 1.358 4.337 11.399 16.596 0.06 0.767 0.051 18.947 1.742 1.016 0.592 1.132 16.049 19.816 2.594 0.78 14.645 1.169 21.563 1.262 0.813 1.376 0.933 2.091 0.563 5.478 9.136 0.558 7.079 1.008 1.153 0.575 0.568 1.258 4.332 4.489 2.887 5.868 1.099 13.697 9.178 0.967 13.796 4.562 16.773 0.198 1.635 0.33 1.494 0.774 9.623 0.271 1.005 17.571 1.848 0.402 2.426 11.48 0.517 0.03 1.301 2.626 15.113 1.596 6.343 16.717 6.25 0.304 1.062 1.163 2.079 1.575 0.234 0.326 3.252 1.368 5.234 10.541 3.802 1.217 15.712 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:218
 Score: 164.195, AlignedPeaks: 299091 398279 561184 724203 884274 1011982 1140247 1303419 1466390 1553257 1716533 
0 226792 228116 258838 260308 271400 278211 285373 297804 299091 316620 370109 396932 397585 398279 402371 416157 417057 498491 515457 516181 533391 543005 559910 560631 561184 597730 611906 660322 662453 663572 679056 706011 724203 755476 758235 772772 787405 788113 826975 859902 869150 883504 884274 901407 914198 918440 919576 922357 931868 933223 948762 997210 1011982 1029492 1033892 1057581 1063464 1064872 1077152 1078124 1101261 1133166 1140247 1149947 1157276 1158531 1159164 1161711 1162451 1173835 1176281 1177709 1179860 1196951 1239975 1240653 1241792 1272615 1293469 1302321 1303419 1308965 1309700 1320323 1325024 1325723 1342724 1366126 1391603 1409386 1411849 1425861 1430063 1433038 1440824 1445200 1452377 1466390 1468852 1486635 1512112 1533554 1535514 1552516 1553257 1557916 1568538 1574819 1575917 1584769 1588021 1588680 1605624 1637585 1638263 1646607 1669127 1698378 1700529 1701957 1704403 1715787 1716533 1719074 1719708 1720962 1728292 1738009 1745073 1776977 1800115 1801086 1809839 1844346 1848745 1866257 1881028 1882208 1929468 1945016 1946370 1955881 1958662 1959798 1964041 1976832 1993964 1994734 2009089 2018337 2051264 2090126 2090833 2105467 2120004 2122762 2154036 2172228 2199183 2214667 2215786 2217917 2297323 2317060 2317608 2335234 2344848 2362058 2362781 2370750 2379748 2461182 2462082 2475868 2479953 2480654 2508130 2532116 2579127 2592865 2600028 2606838 2617930 2619400 2650122 2732252 2860228 
15.0 5.525 7.197 1.533 2.557 2.097 0.891 2.846 2.453 14.431 2.006 2.312 6.14 16.507 19.22 1.955 6.226 0.213 1.35 4.352 5.862 1.186 2.124 2.734 16.356 18.715 0.662 2.648 1.851 3.21 0.925 3.934 4.077 10.824 2.811 3.787 3.989 4.694 2.89 1.284 3.237 2.064 8.84 12.776 6.357 2.018 1.201 2.192 0.037 3.035 3.18 2.564 1.855 5.357 4.125 1.307 1.817 0.56 0.353 2.22 2.705 1.448 1.364 13.813 1.826 0.278 11.411 10.173 13.69 6.052 1.109 4.988 3.805 7.227 1.465 2.563 1.43 2.218 0.059 2.089 3.222 10.386 2.461 1.483 5.027 13.15 4.185 6.769 2.842 1.633 2.73 9.767 2.901 3.558 0.372 1.211 1.314 1.809 18.547 1.318 3.342 2.136 2.467 3.636 10.311 18.169 5.914 1.768 8.787 5.406 0.669 1.371 0.321 1.042 2.752 2.298 0.214 0.869 4.101 4.163 1.926 1.064 8.087 21.957 9.498 9.606 0.656 1.593 12.021 1.963 1.551 2.408 3.195 2.126 0.6 3.662 4.386 6.736 0.777 4.795 3.772 3.174 0.882 1.039 1.101 3.441 6.213 13.124 15.601 2.969 4.72 3.642 3.828 5.721 4.242 3.524 2.824 9.204 9.8 5.415 2.313 5.477 2.983 7.324 8.482 1.901 1.051 0.422 1.431 0.067 0.788 0.853 0.893 0.178 0.276 10.679 0.202 1.257 1.049 16.321 0.972 0.999 1.966 1.859 1.987 2.037 2.288 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:38
 Score: 161.51999999999998, AlignedPeaks: 499126 598169 761170 924213 1084371 1212476 1340685 1503713 1666699 1753716 1916705 
0 200217 212506 228215 271278 271735 283167 289238 299236 315127 339674 428057 434322 452486 499126 509159 521284 542984 553069 570310 570952 597688 598169 614212 620452 631763 670421 684239 701496 760402 761170 770790 784308 800854 820420 847512 869572 879961 923354 924213 949373 958124 975460 993883 1032744 1050627 1068135 1084371 1085412 1102571 1103531 1119848 1155238 1194100 1212476 1229859 1238609 1263675 1264629 1282712 1308022 1311241 1320235 1340685 1343757 1354735 1392574 1393135 1403675 1426799 1427581 1436083 1445664 1473420 1474568 1503713 1517562 1555527 1556221 1573771 1589814 1590295 1607684 1617673 1634914 1636145 1644999 1666699 1678824 1688857 1706876 1720980 1753716 1759924 1764158 1789869 1810542 1833700 1845557 1872856 1888747 1898744 1904816 1916705 1917286 1953600 1959767 2169972 
15.0 2.763 1.319 1.231 10.265 10.747 0.756 3.584 2.448 0.702 0.599 8.229 3.725 2.328 9.187 1.295 3.785 3.645 1.179 3.648 1.002 18.756 18.783 4.851 0.161 2.728 4.814 13.46 0.177 8.199 14.813 0.085 1.804 0.558 4.01 9.383 1.263 0.108 4.242 18.807 2.78 0.236 9.822 3.281 4.187 0.05 0.565 15.731 4.647 8.139 14.578 1.127 0.227 2.101 12.535 1.527 6.702 16.605 2.047 2.018 0.932 1.592 6.48 11.217 0.939 0.368 5.402 3.785 0.265 14.357 0.707 1.01 2.674 0.443 2.381 20.529 5.626 1.372 7.585 6.906 20.649 22.321 9.289 2.886 2.287 1.35 8.835 4.951 1.81 8.021 1.219 5.044 16.238 5.754 0.976 1.442 0.01 0.131 0.567 1.902 1.182 1.463 0.806 18.729 0.937 2.719 1.531 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:155
 Score: 159.393, AlignedPeaks: 499050 598107 761184 924249 1212284 1340371 1503380 1666498 1753558 1916565 
0 271150 287051 289170 305166 307041 308994 314959 321908 370157 381519 410120 421035 427791 434198 449143 452113 467133 469295 499050 508939 521230 553183 598107 598685 614872 631553 662326 683255 683589 684336 721164 761184 811337 847357 861550 896175 905210 924249 936638 948386 963014 970084 975412 978520 1020495 1022409 1052500 1066165 1068418 1076188 1077724 1083774 1085435 1086193 1101521 1119297 1121550 1212284 1241458 1263449 1326165 1333733 1340371 1426527 1454578 1465421 1466551 1503380 1525389 1556161 1589030 1589642 1625649 1634532 1635676 1636778 1666498 1678776 1688674 1718420 1753558 1865807 1872830 1878721 1880674 1882549 1898545 1900664 1916565 2169704 
15.0 13.319 4.169 7.969 7.038 0.866 2.301 9.819 2.551 2.345 0.009 0.294 0.32 7.882 8.18 2.409 7.386 3.939 1.265 7.721 0.212 12.642 0.118 18.782 7.224 0.771 0.348 0.159 3.744 3.281 13.129 0.545 19.579 1.478 15.999 1.24 1.192 1.176 17.105 0.24 1.226 1.413 3.351 12.737 0.601 1.351 1.001 0.861 1.581 1.261 0.565 0.353 3.196 2.506 0.658 1.432 0.595 1.818 15.999 0.053 11.344 0.948 0.407 17.038 11.167 0.07 0.853 0.885 17.182 1.859 1.14 13.187 9.799 0.611 1.213 0.523 1.33 14.141 0.537 5.149 0.627 15.422 3.546 7.663 0.171 0.422 2.555 9.844 5.217 16.424 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:113.311, InsertsAfter: 21
 * M[1] - Mass:99075.84615384616 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:159.763, InsertsAfter: 39
 * M[2] - Mass:262088.0 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:137.52200000000002, InsertsAfter: 31
 * M[3] - Mass:425142.1538461538 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:116.479, InsertsAfter: 20
 * M[4] - Mass:476321.60000000003 Overlap:4/7 LogOddsScore:2.5845964364675087, SumScore:43.397, InsertsAfter: 32
 * M[5] - Mass:584703.8 Overlap:3/7 LogOddsScore:2.5473119882356725, SumScore:27.767, InsertsAfter: 0
 * M[6] - Mass:585838.4615384616 Overlap:7/7 LogOddsScore:8.750161912830762, SumScore:55.885, InsertsAfter: 29
 * M[7] - Mass:713191.6923076924 Overlap:7/7 LogOddsScore:12.382389191831408, SumScore:94.103, InsertsAfter: 28
 * M[8] - Mass:841313.3846153846 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:104.139, InsertsAfter: 48
 * M[9] - Mass:1004371.1538461536 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:113.32199999999999, InsertsAfter: 50
 * M[10] - Mass:1167420.538461538 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:97.633, InsertsAfter: 18
 * M[11] - Mass:1254432.6153846155 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:113.378, InsertsAfter: 61
 * M[12] - Mass:1417530.7692307692 Overlap:7/7 LogOddsScore:14.803874044498507, SumScore:119.23999999999998, InsertsAfter: 27
 * M[13] - Mass:1670673.2 Overlap:4/5 LogOddsScore:8.115426445171428, SumScore:60.0, InsertsAfter: 42
ConsensusPRM: 0 99075 262088 425142 476321 584703 585838 713191 841313 1004371 1167420 1254432 1417530 1670673 Consensus: 0 99075 262088 425142 476321 584703 585838 713191 841313 1004371 1167420 1254432 1417530 1670673
De Novo: VYY[288.049]KYYSY[253.143], Merged: DIVMSQSPSSIAVSVGEKVTMSCKSSQSIIYSSNQKNYIAWYQQKPGQSPKIIIYWASTRESGVPDRFTGSGSGTDFTITISSVKAEDIAVYYCQQYYSY[253.143]
0 115026 228110 327178 458218 545250 673308 760340 857392 944424 1031456 1144540 1215577 1314645 1401677 1500745 1557766 1686808 1814902 1913970 2015017 2146057 2233089 2393173 2521267 2608299 2695331 2823389 2910421 3023505 3136589 3299652 3386684 3473716 3587758 3715816 3843910 3957952 4121015 4234099 4305136 4491215 4654278 4782336 4910394 5038488 5135540 5192561 5320619 5407651 5504703 5632797 5745881 5858965 5972049 6135112 6321191 6392228 6479260 6580307 6736408 6865450 6952482 7009503 7108571 7205623 7320649 7476750 7623818 7724865 7781886 7868918 7925939 8012971 8069992 8171039 8286065 8433133 8534180 8647264 8748311 8861395 8948427 9035459 9134527 9262621 9333658 9462700 9577726 9690810 9761847 9860915 10023978 10187041 10238253 10347125 10347770 10475183 10603241 10766304 10929367 11016399 11179462 11432605 
1185.0 1230.0 1230.0 1230.0 1410.0 1470.0 1515.0 1515.0 1515.0 1530.0 1545.0 1740.0 1680.0 1590.0 1575.0 1575.0 1575.0 1590.0 1275.0 495.0 480.0 570.0 210.0 255.0 300.0 300.0 300.0 300.0 300.0 300.0 270.0 180.0 120.0 120.0 165.0 150.0 165.0 135.0 195.0 255.0 255.0 360.0 360.0 360.0 375.0 435.0 435.0 435.0 435.0 435.0 465.0 945.0 795.0 885.0 810.0 795.0 795.0 780.0 780.0 795.0 780.0 45.0 45.0 45.0 45.0 45.0 45.0 375.0 375.0 390.0 390.0 390.0 390.0 390.0 390.0 390.0 465.0 525.0 525.0 555.0 555.0 540.0 540.0 540.0 540.0 555.0 225.0 225.0 180.0 150.0 86.6555 109.8815 91.26100000000001 73.23949999999999 33.386401237695765 22.20976749179718 55.885 62.0515 67.0695 71.661 63.8165 71.689 74.61999999999999 56.66313374589859 
(RIGHT)Round: 1 for seed: DIVMSQSPSSIAVSVGEKVTMSCKSSQSIIYSSNQKNYIAWYQQKPGQSPKIIIYWASTRESGVPDRFTGSGSGTDFTITISSVKAEDIAVYYCQQYYSY[253.143]
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_1075_0.prm:30
 Score: 189.408, AlignedPeaks: 598130 761170 924251 1212327 1340353 1503409 1666468 1753514 1916672 2169704 
0 201873 208534 271043 271605 287083 287721 289188 299172 305165 308989 315270 316773 395159 398270 402245 427899 433468 434213 436251 452194 467134 478170 497948 499082 521253 553234 570179 598130 598545 614058 630008 662269 683852 684309 721286 733300 760498 761170 793142 825043 847370 870303 896253 899551 900326 924251 934833 936289 941229 974511 975376 1001475 1031650 1066269 1073239 1075833 1076148 1080484 1082081 1084968 1085515 1102747 1105634 1111567 1114476 1121446 1194276 1212327 1246438 1251426 1263452 1340353 1392855 1404480 1409524 1425516 1426545 1454415 1466429 1471548 1503409 1503863 1525446 1573657 1589596 1617536 1626513 1634481 1666468 1678686 1688673 1689767 1753514 1759816 1789444 1870942 1872444 1878725 1881635 1882607 1888543 1897815 1898527 1899994 1900632 1916110 1916672 1979181 1985842 2169704 
15.0 1.989 0.781 14.01 7.252 4.106 2.994 8.456 4.192 13.881 1.559 7.376 1.114 1.972 0.217 2.986 6.127 2.605 9.515 1.178 4.907 2.154 0.107 2.623 10.573 13.917 0.392 1.608 24.031 4.447 0.407 1.06 0.151 14.023 15.973 0.184 1.249 9.124 19.599 0.411 1.085 11.849 0.788 0.479 0.627 0.373 18.18 0.885 0.12 5.268 2.084 11.702 1.325 5.93 0.588 0.804 0.743 0.676 1.548 0.462 1.624 1.561 0.918 0.396 2.169 0.273 1.864 0.115 16.515 2.259 0.177 14.009 15.298 1.322 1.094 0.462 1.411 10.721 1.615 0.523 0.279 17.654 0.118 1.61 2.518 12.724 1.574 0.025 0.936 14.881 0.126 5.933 0.143 16.832 0.643 0.035 0.028 2.069 0.595 0.276 3.911 2.555 1.341 11.394 14.231 5.091 10.812 16.418 0.069 1.529 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Chymotrypsin_0_0_1075_0.prm:10
 Score: 185.909, AlignedPeaks: 598152 761155 924203 1212243 1340351 1503385 1666469 1753502 1916567 2169708 
0 271152 286342 287124 289206 299043 307399 309288 315090 315699 317633 321460 339098 381298 398119 428135 434230 452251 467021 469241 499086 521227 538471 553402 570265 598152 615096 615862 630161 632220 684313 761155 778301 794881 847308 879937 924203 935482 939900 941747 946428 953051 974121 974913 975400 985184 993560 1039303 1066172 1068344 1076556 1078653 1085185 1102533 1121546 1194081 1202534 1212243 1212806 1251257 1263474 1339241 1340351 1343496 1362217 1392838 1409417 1412602 1426552 1466984 1471402 1503385 1525603 1555499 1557557 1589588 1634317 1648453 1649248 1665492 1666469 1678500 1688703 1753502 1759543 1773626 1789599 1848620 1866258 1872628 1878430 1880319 1881478 1882092 1888676 1898512 1900594 1901376 1916567 2169708 
15.0 12.367 1.341 3.557 8.35 5.018 0.745 2.983 6.894 6.716 1.204 3.673 13.24 0.847 0.77 11.448 7.406 6.869 1.358 4.337 11.399 16.596 0.06 0.767 0.051 18.947 1.742 1.016 0.592 1.132 16.049 19.816 2.594 0.78 14.645 1.169 21.563 1.262 0.813 1.376 0.933 2.091 0.563 5.478 9.136 0.558 7.079 1.008 1.153 0.575 0.568 1.258 4.332 4.489 2.887 5.868 1.099 13.697 9.178 0.967 13.796 4.562 16.773 0.198 1.635 0.33 1.494 0.774 9.623 0.271 1.005 17.571 1.848 0.402 2.426 11.48 0.517 0.03 1.301 2.626 15.113 1.596 6.343 16.717 6.25 0.304 1.062 1.163 2.079 1.575 0.234 0.326 3.252 1.368 5.234 10.541 3.802 1.217 15.712 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_725_0.prm:38
 Score: 182.33299999999997, AlignedPeaks: 598169 761170 924213 1084371 1212476 1340685 1503713 1666699 1753716 1916705 2169972 
0 200217 212506 228215 271278 271735 283167 289238 299236 315127 339674 428057 434322 452486 499126 509159 521284 542984 553069 570310 570952 597688 598169 614212 620452 631763 670421 684239 701496 760402 761170 770790 784308 800854 820420 847512 869572 879961 923354 924213 949373 958124 975460 993883 1032744 1050627 1068135 1084371 1085412 1102571 1103531 1119848 1155238 1194100 1212476 1229859 1238609 1263675 1264629 1282712 1308022 1311241 1320235 1340685 1343757 1354735 1392574 1393135 1403675 1426799 1427581 1436083 1445664 1473420 1474568 1503713 1517562 1555527 1556221 1573771 1589814 1590295 1607684 1617673 1634914 1636145 1644999 1666699 1678824 1688857 1706876 1720980 1753716 1759924 1764158 1789869 1810542 1833700 1845557 1872856 1888747 1898744 1904816 1916705 1917286 1953600 1959767 2169972 
15.0 2.763 1.319 1.231 10.265 10.747 0.756 3.584 2.448 0.702 0.599 8.229 3.725 2.328 9.187 1.295 3.785 3.645 1.179 3.648 1.002 18.756 18.783 4.851 0.161 2.728 4.814 13.46 0.177 8.199 14.813 0.085 1.804 0.558 4.01 9.383 1.263 0.108 4.242 18.807 2.78 0.236 9.822 3.281 4.187 0.05 0.565 15.731 4.647 8.139 14.578 1.127 0.227 2.101 12.535 1.527 6.702 16.605 2.047 2.018 0.932 1.592 6.48 11.217 0.939 0.368 5.402 3.785 0.265 14.357 0.707 1.01 2.674 0.443 2.381 20.529 5.626 1.372 7.585 6.906 20.649 22.321 9.289 2.886 2.287 1.35 8.835 4.951 1.81 8.021 1.219 5.044 16.238 5.754 0.976 1.442 0.01 0.131 0.567 1.902 1.182 1.463 0.806 18.729 0.937 2.719 1.531 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1075_0.prm:155
 Score: 181.67200000000003, AlignedPeaks: 598107 761184 924249 1212284 1340371 1503380 1666498 1753558 1916565 2169704 
0 271150 287051 289170 305166 307041 308994 314959 321908 370157 381519 410120 421035 427791 434198 449143 452113 467133 469295 499050 508939 521230 553183 598107 598685 614872 631553 662326 683255 683589 684336 721164 761184 811337 847357 861550 896175 905210 924249 936638 948386 963014 970084 975412 978520 1020495 1022409 1052500 1066165 1068418 1076188 1077724 1083774 1085435 1086193 1101521 1119297 1121550 1212284 1241458 1263449 1326165 1333733 1340371 1426527 1454578 1465421 1466551 1503380 1525389 1556161 1589030 1589642 1625649 1634532 1635676 1636778 1666498 1678776 1688674 1718420 1753558 1865807 1872830 1878721 1880674 1882549 1898545 1900664 1916565 2169704 
15.0 13.319 4.169 7.969 7.038 0.866 2.301 9.819 2.551 2.345 0.009 0.294 0.32 7.882 8.18 2.409 7.386 3.939 1.265 7.721 0.212 12.642 0.118 18.782 7.224 0.771 0.348 0.159 3.744 3.281 13.129 0.545 19.579 1.478 15.999 1.24 1.192 1.176 17.105 0.24 1.226 1.413 3.351 12.737 0.601 1.351 1.001 0.861 1.581 1.261 0.565 0.353 3.196 2.506 0.658 1.432 0.595 1.818 15.999 0.053 11.344 0.948 0.407 17.038 11.167 0.07 0.853 0.885 17.182 1.859 1.14 13.187 9.799 0.611 1.213 0.523 1.33 14.141 0.537 5.149 0.627 15.422 3.546 7.663 0.171 0.422 2.555 9.844 5.217 16.424 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_900_0.prm:17
 Score: 156.5, AlignedPeaks: 1112480 1275464 1438609 1598863 1726615 1854783 2017903 2180741 2268074 2431231 2684167 
0 102809 162955 253180 262257 270973 276285 278786 288061 289411 324163 367180 375160 386129 389261 401300 434152 452707 477203 484288 487252 514116 520263 521340 539503 556228 623619 627220 631725 637724 665394 671442 684274 713272 713877 719436 722285 726351 752084 761253 770059 778377 794895 806359 816282 826702 847317 863240 867640 872767 882299 889201 890992 891622 898187 907681 927346 950354 955416 975562 990530 993482 994268 998432 1008751 1009368 1014957 1058239 1076443 1090321 1090957 1094415 1103365 1112480 1124735 1125522 1134050 1161182 1162510 1176837 1196969 1197606 1206383 1215620 1262361 1263544 1269611 1275464 1292791 1296161 1297538 1299684 1313797 1344688 1357489 1388380 1402493 1404620 1406016 1409386 1426625 1432566 1438609 1439816 1486557 1495116 1495794 1504571 1505208 1525340 1539667 1540995 1568127 1576655 1577442 1589712 1598863 1607762 1611220 1611856 1625734 1643938 1688767 1692809 1693426 1703745 1707909 1708695 1711647 1726615 1746761 1751823 1774831 1786269 1794496 1803990 1810555 1811185 1812976 1819878 1829411 1834537 1854783 1875475 1885895 1895818 1907282 1923776 1940925 1950093 1975826 1979892 1982741 1988300 1988905 2017903 2030735 2036783 2064454 2074958 2078559 2101261 2145949 2180741 2188061 2199948 2214926 2217890 2268074 2285927 2300877 2304167 2312917 2316049 2334998 2412766 2414121 2423392 2425893 2431231 2439920 2447824 2684167 
15.0 1.441 1.059 2.946 2.13 15.694 2.822 4.118 12.16 5.587 2.611 2.882 0.488 1.333 2.764 2.135 11.382 4.358 1.668 1.867 3.474 2.897 3.714 7.932 2.108 3.057 1.822 2.386 3.679 2.291 5.378 3.161 12.471 7.882 6.875 2.576 0.837 1.871 2.168 1.006 0.806 8.866 2.513 0.448 2.458 0.97 9.009 1.627 3.437 1.015 2.149 0.725 1.709 3.178 1.795 4.566 3.11 1.607 1.766 4.891 1.721 1.79 0.58 0.519 0.242 0.191 0.392 2.661 1.463 6.255 0.482 2.13 5.628 13.909 2.605 1.206 3.232 2.903 4.159 2.488 2.313 6.035 2.446 0.77 5.055 12.685 2.103 15.951 0.49 1.936 5.583 1.693 2.98 2.116 1.221 1.642 1.45 5.967 2.026 0.539 16.106 1.758 12.391 2.598 3.793 1.611 2.276 5.861 0.674 1.06 0.87 2.66 4.258 0.14 2.038 16.044 5.765 6.056 0.385 4.85 2.18 5.393 5.299 2.047 2.866 1.934 2.809 1.489 0.947 5.64 1.902 1.889 4.582 0.11 6.249 2.867 4.257 5.574 3.302 1.068 1.467 8.221 7.74 2.064 2.454 2.96 3.904 10.14 1.337 3.348 3.494 1.467 2.651 6.258 7.331 14.299 2.561 3.785 3.089 3.482 2.545 1.022 2.619 15.73 1.365 7.814 1.392 0.992 16.225 0.296 0.348 2.502 0.332 0.625 0.315 1.261 6.501 0.309 0.688 18.85 1.251 0.946 15.0 

SpectrumHMM Model: * M[0] - Mass:-87.45454545454545 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:204.3065, InsertsAfter: 43
 * M[1] - Mass:163023.18181818182 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:181.019, InsertsAfter: 38
 * M[2] - Mass:326091.0 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:161.28549999999998, InsertsAfter: 19
 * M[3] - Mass:377263.22222222225 Overlap:4/7 LogOddsScore:2.5845964364675087, SumScore:43.397, InsertsAfter: 39
 * M[4] - Mass:486721.63636363635 Overlap:7/7 LogOddsScore:7.539419486497213, SumScore:52.16776749179718, InsertsAfter: 8
 * M[5] - Mass:504626.6666666667 Overlap:3/7 LogOddsScore:2.5473119882356725, SumScore:19.985, InsertsAfter: 22
 * M[6] - Mass:614187.0909090908 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:126.43749999999999, InsertsAfter: 31
 * M[7] - Mass:742290.0909090909 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:135.1355, InsertsAfter: 43
 * M[8] - Mass:905337.1818181819 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:158.896, InsertsAfter: 41
 * M[9] - Mass:1068375.3636363638 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:128.6325, InsertsAfter: 16
 * M[10] - Mass:1155438.6363636365 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:153.123, InsertsAfter: 54
 * M[11] - Mass:1318518.090909091 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:160.753, InsertsAfter: 7
 * M[12] - Mass:1571633.6363636362 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:131.6631337458986, InsertsAfter: 0
ConsensusPRM: -87 163023 326091 377263 486721 504626 614187 742290 905337 1068375 1155438 1318518 1571633 Consensus: -87 163023 326091 377263 486721 504626 614187 742290 905337 1068375 1155438 1318518 1571633
De Novo: YY[288.096]KYYSY[253.115], Merged: DIVMSQSPSSIAVSVGEKVTMSCKSSQSIIYSSNQKNYIAWYQQKPGQSPKIIIYWASTRESGVPDRFTGSGSGTDFTITISSVKAEDIAVYYCQQYYSY[253.143]
0 115026 228110 327178 458218 545250 673308 760340 857392 944424 1031456 1144540 1215577 1314645 1401677 1500745 1557766 1686808 1814902 1913970 2015017 2146057 2233089 2393173 2521267 2608299 2695331 2823389 2910421 3023505 3136589 3299652 3386684 3473716 3587758 3715816 3843910 3957952 4121015 4234099 4305136 4491215 4654278 4782336 4910394 5038488 5135540 5192561 5320619 5407651 5504703 5632797 5745881 5858965 5972049 6135112 6321191 6392228 6479260 6580307 6736408 6865450 6952482 7009503 7108571 7205623 7320649 7476750 7623818 7724865 7781886 7868918 7925939 8012971 8069992 8171039 8286065 8433133 8534180 8647264 8748311 8861395 8948427 9035459 9134527 9262621 9333658 9462700 9577726 9690810 9761847 9860915 10023978 10187041 10238235 10347125 10347693 10365598 10475183 10603241 10766304 10929367 11016399 11179462 11432605 
1185.0 1230.0 1230.0 1230.0 1410.0 1470.0 1515.0 1515.0 1515.0 1530.0 1545.0 1740.0 1680.0 1590.0 1575.0 1575.0 1575.0 1590.0 1275.0 495.0 480.0 570.0 210.0 255.0 300.0 300.0 300.0 300.0 300.0 300.0 270.0 180.0 120.0 120.0 165.0 150.0 165.0 135.0 195.0 255.0 255.0 360.0 360.0 360.0 375.0 435.0 435.0 435.0 435.0 435.0 465.0 945.0 795.0 885.0 810.0 795.0 795.0 780.0 780.0 795.0 780.0 45.0 45.0 45.0 45.0 45.0 45.0 375.0 375.0 390.0 390.0 390.0 390.0 390.0 390.0 390.0 465.0 525.0 525.0 555.0 555.0 540.0 540.0 540.0 540.0 555.0 225.0 225.0 180.0 150.0 86.6555 157.094 136.14000000000001 117.26249999999999 33.386401237695765 22.20976749179718 52.16776749179718 6.63753498359436 94.24449999999999 101.1025 115.2785 96.22449999999999 112.40599999999999 117.6865 94.16313374589859 

(LEFT)Round: 0 for seed: TFGGGTKLEIK
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:383
 Score: 134.118, AlignedPeaks: 1068386 1169308 1316447 1373488 1430511 1487505 1588742 1716833 1830064 1958728 
0 144440 146674 173674 239239 241414 257404 259969 382144 382664 387886 388339 400181 401898 403403 413204 420002 449114 473379 488363 489227 495327 513313 517068 532378 546233 564987 580937 589074 603233 625810 633971 642315 660291 662214 673425 677400 682213 684759 686873 697099 705967 715196 774199 787504 794426 804967 807444 815022 823112 825340 835456 849511 859667 869032 901532 905891 907157 908352 911287 911866 915032 916149 925834 930124 936378 958276 1040359 1061706 1064756 1065451 1068386 1070847 1075206 1117071 1118307 1127227 1141282 1151398 1161716 1169308 1171771 1179701 1182312 1189234 1261542 1270771 1289854 1294525 1299338 1314524 1316447 1327488 1332311 1334423 1342767 1373488 1395801 1397110 1400905 1404916 1411751 1430511 1444360 1459669 1463424 1481411 1487505 1488375 1503359 1563534 1573335 1574939 1576557 1588742 1594594 1602766 1646478 1655368 1684113 1699022 1708580 1716833 1722492 1732603 1747631 1803064 1811782 1830064 1958728 
15.0 1.774 7.458 1.809 13.042 0.667 1.925 17.212 10.077 2.774 5.68 4.242 3.771 14.807 0.466 0.745 3.765 0.291 1.353 4.713 6.104 1.236 2.465 0.047 0.697 11.594 9.227 2.98 1.552 13.579 0.893 0.743 3.722 11.787 1.08 0.823 3.87 1.305 0.542 10.165 0.051 2.98 4.089 0.55 0.988 2.294 5.094 17.438 17.958 1.973 6.831 1.06 0.766 1.042 0.539 1.183 0.111 1.213 6.738 11.395 14.456 2.777 1.076 1.144 1.651 0.325 2.683 0.369 4.577 11.755 7.979 4.443 0.438 1.158 0.466 2.29 1.005 0.267 1.942 12.443 18.539 11.479 7.143 0.316 3.084 1.805 6.395 10.671 0.639 1.456 0.677 14.046 1.569 3.341 10.149 1.297 10.466 5.876 0.923 0.182 1.017 12.246 15.943 0.744 1.501 3.048 1.911 6.781 4.404 1.671 1.001 1.184 13.096 3.618 12.202 7.351 0.755 0.39 0.337 1.419 1.938 0.265 15.512 0.585 0.208 1.681 2.046 1.846 6.186 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_600_0.prm:808
 Score: 109.01100000000001, AlignedPeaks: 940319 1041422 1188541 1245429 1302660 1460723 1588717 1702100 1830869 
0 146779 203804 260161 260583 292836 316683 321264 330333 432472 437006 473230 481174 485325 490354 524183 525169 546229 547347 558128 560328 574046 603240 618115 660296 662238 675200 686900 692484 705832 709531 721288 747952 784132 794148 805601 807457 813663 825432 847058 859941 861505 901535 908479 924463 940319 947344 997829 1001821 1026316 1041422 1043279 1071968 1082781 1127591 1142430 1143047 1156395 1161979 1173679 1179929 1185999 1186641 1188541 1199460 1230764 1243688 1245429 1254496 1263602 1267960 1276900 1290751 1301532 1302660 1316426 1323710 1324695 1342823 1358525 1363554 1367705 1375649 1411873 1416407 1439891 1445137 1448328 1454062 1460723 1488801 1518546 1527615 1536618 1547158 1556043 1564511 1574915 1588296 1588717 1602747 1604362 1645112 1662830 1694116 1702100 1830869 
15.0 5.743 15.912 5.804 4.055 3.426 1.463 2.351 1.892 0.392 9.934 0.927 1.222 0.331 1.856 8.536 5.439 5.734 6.967 0.399 0.447 1.318 5.973 2.915 20.614 2.033 1.704 15.929 2.643 4.496 1.327 1.243 1.355 6.301 0.675 3.836 12.656 0.457 2.14 0.475 0.887 0.754 8.208 5.856 4.71 4.509 3.459 1.333 0.094 1.867 11.536 4.532 4.106 2.685 0.276 0.028 4.363 0.884 11.47 1.836 4.133 0.601 5.152 22.594 0.053 2.542 0.291 11.396 0.563 7.762 1.903 0.333 0.207 6.246 8.536 1.633 4.868 5.261 0.689 1.304 0.197 1.171 2.681 6.263 0.19 0.321 1.403 0.632 1.076 9.696 1.431 5.491 4.27 1.071 1.499 5.99 0.403 0.688 5.262 6.595 0.299 1.371 12.347 2.859 1.333 4.149 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_875_0.prm:32
 Score: 91.447, AlignedPeaks: 1347404 1404241 1518381 1619322 1747533 
0 128058 189945 225750 226815 228807 245089 245866 247188 263387 265337 287073 360005 361270 378839 418168 436321 440240 445751 454264 474986 515225 564130 603243 604285 621019 661295 679290 748308 755228 766250 776310 784338 791170 793216 860247 891591 896980 899628 900396 904222 905296 992354 1017223 1104259 1125132 1144524 1161266 1162300 1171452 1201413 1245480 1248593 1290557 1303096 1311279 1319035 1319792 1325303 1346809 1347404 1404241 1500206 1518381 1519677 1520454 1536736 1539793 1575598 1619322 1747533 
15.0 0.393 1.488 0.992 9.799 3.312 1.195 3.442 8.166 0.386 2.722 2.891 1.078 7.939 3.603 17.095 10.565 0.496 1.397 0.422 2.701 1.438 0.877 0.557 8.831 0.153 8.206 3.7 13.095 0.768 11.285 4.213 2.745 5.649 2.422 0.049 7.807 1.14 1.736 5.335 5.36 1.358 1.876 22.806 19.575 0.097 0.167 15.615 2.009 0.25 1.483 0.972 0.659 1.099 1.086 0.657 0.533 1.08 0.113 0.616 22.526 14.697 0.476 12.726 8.043 5.735 5.302 3.263 2.633 11.498 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_575_0.prm:844
 Score: 87.319, AlignedPeaks: 416260 517399 664348 778844 936454 1064473 1177705 
0 131243 163020 259255 259918 277389 287369 303440 343066 346949 360336 416260 417554 422235 474313 489735 517399 520895 531386 606246 606947 615740 620409 654477 663346 664348 672480 679386 694240 727961 736258 741319 744644 773481 778844 779472 786259 797652 804319 835351 870575 917854 918327 936454 1064473 1177705 
15.0 12.606 3.74 26.873 11.25 20.186 5.575 1.727 0.931 1.522 10.168 11.15 4.056 1.035 3.931 0.453 1.797 1.494 8.93 0.449 2.897 3.214 1.611 3.558 3.482 4.003 2.987 1.765 3.004 1.666 2.262 1.677 1.68 0.174 1.615 10.669 0.062 1.175 2.282 3.584 3.044 1.579 0.935 26.435 12.319 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_925_0.prm:2
 Score: 86.642, AlignedPeaks: 1188465 1245456 1302510 1359431 1460550 1588638 1701605 1830625 
0 147030 257903 259995 273704 275940 277814 278666 284593 285272 371064 386029 388125 388793 400284 406184 432069 437013 489235 513182 524078 546126 580914 603255 658150 660215 684810 687107 697148 705139 784142 787336 788063 801158 807237 833091 834086 835359 837085 851542 908383 932547 933253 947178 965227 996649 997094 997583 1006061 1006451 1006735 1011551 1015544 1060572 1061299 1063062 1142507 1151487 1177627 1186000 1188465 1190485 1216081 1225152 1245456 1259443 1267722 1281543 1302510 1304512 1324591 1335453 1342587 1353264 1359431 1411633 1416567 1459842 1460550 1574931 1580604 1588638 1590732 1660593 1699678 1701605 1830625 
15.0 12.723 4.807 14.581 2.742 0.226 5.134 1.404 0.519 0.454 4.925 1.42 12.985 5.891 0.094 1.302 1.62 6.255 7.81 0.108 11.883 3.192 0.386 6.527 1.522 10.882 2.384 17.19 1.719 0.804 5.438 0.19 0.463 0.55 3.183 0.082 7.473 0.917 1.583 0.136 0.753 2.436 2.969 3.454 0.867 1.649 8.969 11.306 3.058 3.988 0.961 2.48 2.473 0.353 2.12 1.458 2.253 0.742 0.495 4.608 3.411 0.16 1.16 0.977 2.641 0.577 2.973 0.605 0.59 0.177 12.604 0.674 11.799 0.488 3.721 6.089 1.099 9.934 17.442 1.248 0.197 16.763 8.754 1.48 0.778 12.074 15.0 

SpectrumHMM Model: * M[0] - Mass:-940334.5 Overlap:2/3 LogOddsScore:3.885748146743283, SumScore:30.0, InsertsAfter: 1
 * M[1] - Mass:-680335.4999999999 Overlap:3/3 LogOddsScore:3.923032594975119, SumScore:26.064999999999998, InsertsAfter: 13
 * M[2] - Mass:-666567.0 Overlap:2/3 LogOddsScore:2.675005720409734, SumScore:17.549, InsertsAfter: 3
 * M[3] - Mass:-503352.2 Overlap:3/3 LogOddsScore:2.7122901686415704, SumScore:25.416, InsertsAfter: 29
 * M[4] - Mass:-416216.50000000006 Overlap:3/4 LogOddsScore:3.5791024432902576, SumScore:35.419, InsertsAfter: 12
 * M[5] - Mass:-280239.6 Overlap:3/4 LogOddsScore:3.5791024432902576, SumScore:32.484, InsertsAfter: 24
 * M[6] - Mass:-253341.39999999997 Overlap:4/4 LogOddsScore:7.24861417052274, SumScore:54.81700000000001, InsertsAfter: 6
 * M[7] - Mass:-156481.46153846153 Overlap:4/4 LogOddsScore:6.291009380269713, SumScore:53.068, InsertsAfter: 18
 * M[8] - Mass:0.0 Overlap:5/6 LogOddsScore:7.104313587545898, SumScore:125.102, InsertsAfter: 40
 * M[9] - Mass:101042.07142857145 Overlap:5/6 LogOddsScore:8.315056013879445, SumScore:166.87199999999999, InsertsAfter: 26
 * M[10] - Mass:248125.82352941178 Overlap:6/6 LogOddsScore:10.77382531477838, SumScore:209.05399999999997, InsertsAfter: 37
 * M[11] - Mass:305097.1428571429 Overlap:5/6 LogOddsScore:7.104313587545898, SumScore:189.50300000000001, InsertsAfter: 13
 * M[12] - Mass:362284.93750000006 Overlap:6/6 LogOddsScore:9.563082888444832, SumScore:191.68400000000003, InsertsAfter: 19
 * M[13] - Mass:419108.33333333343 Overlap:5/6 LogOddsScore:7.104313587545898, SumScore:179.086, InsertsAfter: 18
 * M[14] - Mass:520296.4705882353 Overlap:6/6 LogOddsScore:11.026962950858902, SumScore:230.775, InsertsAfter: 21
 * M[15] - Mass:648353.1176470586 Overlap:6/6 LogOddsScore:10.77382531477838, SumScore:216.189, InsertsAfter: 18
 * M[16] - Mass:761596.4375 Overlap:6/6 LogOddsScore:9.563082888444832, SumScore:202.40900000000002, InsertsAfter: 13
 * M[17] - Mass:890419.6153846155 Overlap:5/5 LogOddsScore:11.080471018231405, SumScore:210.0, InsertsAfter: 0
 * M[18] - Mass:1003529.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:165.0, InsertsAfter: 0
ConsensusPRM: -940334 -680335 -666567 -503352 -416216 -280239 -253341 -156481 0 101042 248125 305097 362284 419108 520296 648353 761596 890419 1003529 Consensus: -940334 -680335 -666567 -503352 -416216 -280239 -253341 -156481 0 101042 248125 305097 362284 419108 520296 648353 761596 890419 1003529
De Novo: [273.767]YSYPRTFGGGTQIEI, Merged: [273.767]YSYPRTFGGGTQIEIK
-940334 -680335 -666567 -503352 -416216 -280239 -253341 -156481 0 101042 248125 305097 362284 419108 520296 648353 761596 890419 1003529 1131623 
30.0 26.064999999999998 17.549 25.416 35.419 32.484 54.81700000000001 53.068 115.051 150.93599999999998 187.027 177.25150000000002 178.342 172.043 197.8875 190.59449999999998 183.7045 187.5 165.0 165.0 
(RIGHT)Round: 0 for seed: [273.767]YSYPRTFGGGTQIEIK
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:12
 Score: 151.945, AlignedPeaks: 0 146841 204144 261064 318100 419259 547252 660360 789342 902424 1030573 
0 146841 147103 204144 259226 261064 318100 388235 406223 419259 463283 501308 508384 533262 542604 547252 597676 606435 625641 626247 641136 647420 660360 675337 678322 755373 787519 788745 789342 844437 901480 901742 902424 1030573 
15.0 10.572 8.117 13.554 19.267 4.54 2.858 16.506 4.465 2.889 3.837 4.703 0.781 2.739 1.44 7.51 4.379 0.93 1.504 3.884 0.369 1.47 13.219 0.464 1.191 0.642 4.609 7.072 23.445 9.476 14.306 17.555 13.358 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:199
 Score: 126.064, AlignedPeaks: 248144 305185 362254 419045 520327 648269 761370 890337 1003464 1131613 
0 174109 218044 248144 302256 305185 320372 362254 400086 415354 419045 422327 519813 520327 544337 550375 562330 630357 642378 648269 661640 670595 674628 675365 679208 683677 691743 692439 702792 703400 761370 776788 785447 785909 805198 814301 821545 833953 872351 883395 885968 890337 905636 923426 943468 1000530 1003464 1057572 1085527 1131613 1287712 
15.0 7.306 1.223 31.392 18.389 17.634 1.207 2.816 0.205 12.2 6.672 1.379 15.23 14.146 6.499 3.087 2.583 0.444 0.627 1.384 7.405 3.81 6.959 2.454 2.771 0.972 0.805 0.019 0.607 2.537 13.628 8.849 8.716 8.367 2.991 0.673 2.553 1.885 0.599 0.126 0.233 16.559 1.627 0.74 0.389 4.1 10.372 17.254 2.524 11.461 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:157
 Score: 124.36099999999999, AlignedPeaks: 0 114570 171210 272213 400307 513337 642349 755350 883389 
0 114570 171210 174280 226158 271395 272213 302384 320355 338438 350435 359266 399265 400307 415365 433387 433999 451393 513337 537926 544363 546692 550819 555480 557386 558860 585898 606325 614352 642349 664929 699458 737363 755350 756485 786155 789582 803482 883389 1039708 
15.0 2.209 6.138 14.34 0.765 7.393 16.674 10.824 1.449 1.234 0.734 1.196 1.562 12.916 7.773 1.795 1.853 1.601 11.862 3.035 3.342 4.28 1.322 0.546 0.45 1.093 2.833 0.005 2.932 15.021 2.673 0.78 0.681 11.376 0.306 6.004 2.27 12.567 18.165 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/Orbi/3F12_Orbi_Other_0_0_525_0.prm:17
 Score: 114.775, AlignedPeaks: 0 147059 204083 318132 419177 547271 660359 789398 1030573 
0 147059 204083 259185 277196 295208 318132 350183 388226 406247 419177 463272 501313 509248 533295 547271 597321 597824 625831 626334 660359 789398 844501 901524 1030573 
15.0 5.933 9.046 18.989 0.645 0.8 2.188 2.94 12.724 4.11 4.684 3.775 4.731 0.147 1.892 6.461 1.603 3.692 0.762 2.547 7.448 19.015 4.544 1.011 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_425_0.prm:65
 Score: 109.756, AlignedPeaks: 100676 247926 305117 520063 648396 761406 890375 1003466 1131650 
0 100676 245944 247926 302273 305117 319399 320159 397331 415305 418470 421229 422471 475411 500430 520063 531191 544355 550321 562354 634313 642335 647815 648396 657386 657941 663421 703216 761406 774565 775850 776838 785676 805326 833909 876385 881904 882603 883285 885134 887286 890375 901284 904070 908425 952891 976922 985597 987392 1000639 1003466 1018526 1057835 1085611 1088698 1098033 1129518 1131650 1174503 1287746 
15.0 7.425 0.615 24.339 8.933 10.059 0.597 1.968 3.351 9.184 2.654 1.876 4.405 5.102 1.686 10.463 0.534 14.134 2.073 0.624 0.799 0.524 9.578 12.13 7.041 3.501 1.407 0.403 14.029 0.628 0.247 3.015 8.173 5.559 0.184 1.955 0.969 0.493 0.25 0.196 0.767 13.048 0.902 2.916 3.108 5.254 0.7 0.573 0.096 6.159 10.67 0.865 3.52 7.771 0.008 0.881 4.502 7.593 0.733 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:5/5 LogOddsScore:9.869728591897857, SumScore:188.361, InsertsAfter: 3
 * M[1] - Mass:147045.11111111112 Overlap:7/7 LogOddsScore:13.141802100072974, SumScore:274.263, InsertsAfter: 3
 * M[2] - Mass:204159.2857142857 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:227.5445, InsertsAfter: 4
 * M[3] - Mass:261030.875 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:206.89600000000002, InsertsAfter: 6
 * M[4] - Mass:318082.8888888889 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:192.553, InsertsAfter: 13
 * M[5] - Mass:419159.1111111111 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:247.8275, InsertsAfter: 28
 * M[6] - Mass:547333.5555555555 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:230.99549999999996, InsertsAfter: 28
 * M[7] - Mass:660424.5555555557 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:243.89049999999997, InsertsAfter: 37
 * M[8] - Mass:789397.1111111111 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:274.58799999999997, InsertsAfter: 20
 * M[9] - Mass:902474.625 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:210.776, InsertsAfter: 12
 * M[10] - Mass:1030591.3333333333 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:232.219, InsertsAfter: 1
 * M[11] - Mass:1186790.8 Overlap:3/3 LogOddsScore:6.344517447642216, SumScore:45.0, InsertsAfter: 0
ConsensusPRM: 0 147045 204159 261030 318082 419159 547333 660424 789397 902474 1030591 1186790 Consensus: 0 147045 204159 261030 318082 419159 547333 660424 789397 902474 1030591 1186790
De Novo: FGGGTKIEIKR, Merged: [273.767]YSYPRTFGGGTQIEIKR
-940334 -666567 -503352 -416216 -253341 -156481 0 101042 248125 305097 362284 419108 520296 648353 761596 890419 1003529 1131623 1287822 
30.0 17.549 25.416 35.419 54.81700000000001 53.068 115.051 169.64849999999998 230.64499999999998 200.7295668729493 190.9505668729493 182.298 222.8575 210.79499999999996 213.79749999999999 231.04399999999998 186.21956687294931 198.6095 45.0 
(RIGHT)Round: 1 for seed: [273.767]YSYPRTFGGGTQIEIKR
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_650_0.prm:199
 Score: 156.064, AlignedPeaks: 248144 305185 362254 419045 520327 648269 761370 890337 1003464 1131613 1287712 
0 174109 218044 248144 302256 305185 320372 362254 400086 415354 419045 422327 519813 520327 544337 550375 562330 630357 642378 648269 661640 670595 674628 675365 679208 683677 691743 692439 702792 703400 761370 776788 785447 785909 805198 814301 821545 833953 872351 883395 885968 890337 905636 923426 943468 1000530 1003464 1057572 1085527 1131613 1287712 
15.0 7.306 1.223 31.392 18.389 17.634 1.207 2.816 0.205 12.2 6.672 1.379 15.23 14.146 6.499 3.087 2.583 0.444 0.627 1.384 7.405 3.81 6.959 2.454 2.771 0.972 0.805 0.019 0.607 2.537 13.628 8.849 8.716 8.367 2.991 0.673 2.553 1.885 0.599 0.126 0.233 16.559 1.627 0.74 0.389 4.1 10.372 17.254 2.524 11.461 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_525_0.prm:157
 Score: 154.361, AlignedPeaks: 0 114570 171210 272213 400307 513337 642349 755350 883389 1039708 
0 114570 171210 174280 226158 271395 272213 302384 320355 338438 350435 359266 399265 400307 415365 433387 433999 451393 513337 537926 544363 546692 550819 555480 557386 558860 585898 606325 614352 642349 664929 699458 737363 755350 756485 786155 789582 803482 883389 1039708 
15.0 2.209 6.138 14.34 0.765 7.393 16.674 10.824 1.449 1.234 0.734 1.196 1.562 12.916 7.773 1.795 1.853 1.601 11.862 3.035 3.342 4.28 1.322 0.546 0.45 1.093 2.833 0.005 2.932 15.021 2.673 0.78 0.681 11.376 0.306 6.004 2.27 12.567 18.165 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_425_0.prm:65
 Score: 132.33100000000002, AlignedPeaks: 247926 305117 520063 648396 761406 890375 1003466 1131650 1287746 
0 100676 245944 247926 302273 305117 319399 320159 397331 415305 418470 421229 422471 475411 500430 520063 531191 544355 550321 562354 634313 642335 647815 648396 657386 657941 663421 703216 761406 774565 775850 776838 785676 805326 833909 876385 881904 882603 883285 885134 887286 890375 901284 904070 908425 952891 976922 985597 987392 1000639 1003466 1018526 1057835 1085611 1088698 1098033 1129518 1131650 1174503 1287746 
15.0 7.425 0.615 24.339 8.933 10.059 0.597 1.968 3.351 9.184 2.654 1.876 4.405 5.102 1.686 10.463 0.534 14.134 2.073 0.624 0.799 0.524 9.578 12.13 7.041 3.501 1.407 0.403 14.029 0.628 0.247 3.015 8.173 5.559 0.184 1.955 0.969 0.493 0.25 0.196 0.767 13.048 0.902 2.916 3.108 5.254 0.7 0.573 0.096 6.159 10.67 0.865 3.52 7.771 0.008 0.881 4.502 7.593 0.733 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_650_0.prm:29
 Score: 109.464, AlignedPeaks: 248167 305130 362335 419141 520062 761189 890335 1003484 1131461 1287712 
0 167795 174261 216423 246708 247324 248167 268802 286613 287072 302224 305130 315070 362335 391676 409231 415352 419141 517913 520062 520602 544585 555825 562338 571361 661217 661999 663645 665492 669442 671664 675022 703286 742709 761189 776837 785690 794310 804718 805464 817654 840150 871654 880397 881396 890335 902699 914689 919753 943421 970894 972473 980562 1000592 1003484 1018650 1057555 1059014 1085624 1131461 1159277 1287712 
15.0 0.543 5.313 1.157 1.759 10.504 21.372 0.855 8.394 8.282 10.221 9.707 1.012 8.272 1.973 0.041 10.418 2.183 0.252 4.23 2.364 6.778 5.957 3.305 2.333 0.339 9.017 1.478 0.615 1.32 5.789 3.156 2.521 3.004 9.543 8.485 7.554 2.193 0.801 4.745 0.041 0.597 1.327 3.136 2.576 10.958 0.057 3.83 1.359 3.601 1.268 1.653 0.427 1.242 6.196 15.42 0.513 0.233 4.746 7.003 2.7 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_575_0.prm:26
 Score: 103.372, AlignedPeaks: 0 112991 242201 355204 483329 
0 112991 127618 128092 128767 241345 242201 247254 304235 355204 373247 388308 418235 425082 483329 489348 501270 527355 583565 583965 584355 584734 592601 605632 631200 640119 660282 666304 694631 695744 704708 717530 731403 752256 760552 761302 775912 779408 788363 794407 807302 845303 885633 902385 907404 1003230 1003495 1131620 
15.0 6.893 0.948 1.645 0.096 11.461 34.76 2.047 1.027 15.797 0.958 3.572 2.966 1.702 15.922 1.582 4.072 0.412 2.986 0.4 2.483 2.053 3.35 0.547 1.043 3.745 0.609 1.285 0.012 7.535 3.614 0.58 9.65 3.006 0.233 5.711 1.663 2.107 1.928 8.544 2.505 5.005 1.211 9.457 27.881 7.371 7.95 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:6/6 LogOddsScore:13.448447803526, SumScore:322.748, InsertsAfter: 6
 * M[1] - Mass:57041.75 Overlap:5/6 LogOddsScore:8.315056013879445, SumScore:238.1295668729493, InsertsAfter: 4
 * M[2] - Mass:114251.75 Overlap:5/6 LogOddsScore:7.104313587545898, SumScore:204.2475668729493, InsertsAfter: 7
 * M[3] - Mass:170922.40000000002 Overlap:6/6 LogOddsScore:8.352340462111282, SumScore:199.945, InsertsAfter: 9
 * M[4] - Mass:272017.0 Overlap:6/6 LogOddsScore:10.77382531477838, SumScore:269.4545, InsertsAfter: 24
 * M[5] - Mass:400271.6 Overlap:6/7 LogOddsScore:10.42989516309352, SumScore:252.22499999999994, InsertsAfter: 27
 * M[6] - Mass:513292.5 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:269.75249999999994, InsertsAfter: 46
 * M[7] - Mass:642313.6666666666 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:321.39, InsertsAfter: 25
 * M[8] - Mass:755393.8333333335 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:240.63056687294932, InsertsAfter: 20
 * M[9] - Mass:883488.5 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:258.75350000000003, InsertsAfter: 12
 * M[10] - Mass:1039780.8333333333 Overlap:7/7 LogOddsScore:13.593131618164957, SumScore:108.745, InsertsAfter: 22
ConsensusPRM: 0 57041 114251 170922 272017 400271 513292 642313 755393 883488 1039780 Consensus: 0 57041 114251 170922 272017 400271 513292 642313 755393 883488 1039780
De Novo: GGGTKIEIKR, Merged: [273.767]YSYPRTFGGGTQIEIKR
-940334 -666567 -503352 -416216 -253341 -156481 0 101042 248125 305097 362284 419108 520296 648353 761596 890419 1003529 1131623 1287822 
30.0 17.549 25.416 35.419 54.81700000000001 53.068 115.051 169.64849999999998 276.6965 217.7611337458986 195.9306337458986 191.1215 246.156 229.84156687294924 241.77499999999998 276.217 213.42506687294932 228.68150000000003 76.8725 

(LEFT)Round: 0 for seed: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1400_0.prm:8
 Score: 95.432, AlignedPeaks: 526424 597526 712310 783324 854374 951138 1052479 1151532 1351714 
0 98627 128235 146953 241525 377185 389337 391240 406641 449065 459871 460944 468173 476153 486333 491690 494183 497213 508311 511107 512325 526424 547381 570296 577379 583307 591363 595503 597526 599303 608023 612398 614549 625223 644332 694331 712310 738363 765442 783324 808561 818275 826398 828770 829456 836390 847944 854374 889649 908429 915275 916486 926203 947237 951138 965091 969437 976058 988918 1016478 1033223 1034501 1039939 1052479 1107443 1133404 1150932 1151532 1152183 1160003 1169023 1186226 1186906 1203774 1212426 1218499 1236264 1238243 1286332 1305444 1315472 1333462 1342977 1343455 1348940 1351714 1355649 1357781 1360322 1424686 1456408 1462481 1465249 1470734 1471212 1474248 1480773 1498195 1498762 1508745 1517881 1527857 1595694 1601763 1610415 1645166 1654186 1662006 1662666 1663257 1680785 1695543 1702776 1706746 1746201 1751933 1761811 1779720 1780966 1797614 1825271 1844752 1959822 1977827 1987791 1995987 2005628 2030865 2048748 2075826 2101880 2119859 2169857 2287765 2322500 2337985 2422949 
15.0 3.05 0.724 1.322 2.589 2.791 2.399 2.882 1.673 3.328 2.298 3.186 4.821 8.071 5.375 0.635 5.368 5.879 3.249 7.247 4.83 6.43 3.889 4.342 6.823 4.373 3.656 5.377 5.045 6.618 5.443 7.035 6.726 9.5 3.125 3.082 7.741 3.023 2.802 4.59 2.806 8.917 1.257 0.435 0.946 3.091 0.256 21.169 13.586 0.844 0.399 0.207 2.842 1.905 0.847 0.145 0.548 0.13 0.583 0.666 0.891 15.538 0.534 15.092 0.315 1.831 9.763 21.444 0.786 0.236 1.223 1.187 2.054 0.03 0.599 8.313 1.616 2.423 0.221 0.317 14.314 17.586 6.813 6.813 0.201 13.074 1.936 1.105 0.73 6.925 0.591 6.658 2.753 6.575 7.282 2.473 2.078 17.322 19.126 2.135 0.919 2.097 11.904 1.097 1.995 10.901 0.616 6.317 19.71 1.704 6.284 1.064 1.044 3.125 0.979 1.232 9.905 16.513 0.147 0.293 0.321 1.963 17.547 8.764 2.41 14.139 2.803 2.866 1.492 2.661 6.33 3.411 1.282 1.86 0.691 0.022 2.63 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_950_0.prm:80
 Score: 90.233, AlignedPeaks: 241263 397267 468359 583350 654393 725333 923237 
0 128877 160146 172072 239275 241263 244298 256208 258261 267307 275395 276363 282847 286262 295243 299925 301276 323196 325283 328629 338401 342185 369434 370987 387023 395114 397267 408329 413202 415333 440168 453229 466088 468359 481272 484246 486351 532208 537268 581272 583350 613362 626441 654393 683707 684276 691360 708214 709453 712404 723349 725333 743462 799422 803851 821318 826976 832901 836198 866156 868781 884431 923237 935352 962241 968510 970731 971579 975270 983694 1016927 1017709 1026299 1035347 1035990 1038150 1040775 1070640 1073314 1074030 1085613 1103080 1163469 1181597 1194527 1197478 1208567 1222718 1223224 1252576 1293569 1321472 1323597 1369650 1391646 1395504 1420591 1421667 1425659 1438600 1453702 1466763 1498602 1509684 1537497 1624084 1631536 1648670 1650723 1662633 1734859 1744718 1746785 1888921 
15.0 8.629 0.343 0.917 7.968 11.38 2.337 0.898 6.645 2.137 0.632 0.315 3.314 2.926 2.372 3.661 2.212 0.244 0.239 2.498 0.933 1.323 0.307 4.48 5.683 4.621 20.354 0.868 1.651 4.829 0.071 0.741 0.562 11.92 0.28 1.704 5.503 2.236 4.916 5.302 18.342 0.694 0.134 10.791 4.16 4.915 0.371 3.124 0.9 2.346 2.538 17.214 0.809 2.113 2.633 0.931 0.902 0.716 9.577 0.87 2.693 2.701 0.232 0.228 10.679 1.877 4.345 1.253 4.022 2.444 1.233 7.072 2.34 1.663 1.668 0.201 0.559 6.972 4.17 3.089 0.163 0.281 0.64 14.923 0.715 1.386 0.864 5.321 3.893 6.678 0.796 0.016 17.626 7.866 3.286 2.471 6.771 1.091 1.947 5.956 0.671 2.429 1.527 18.928 0.105 1.094 0.574 7.133 1.014 1.218 1.543 0.982 0.766 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1000_0.prm:89
 Score: 87.38899999999998, AlignedPeaks: 370119 526451 597463 712446 783461 854470 1052592 1151565 1238555 1351640 
0 226698 240526 242032 252893 260214 267182 269145 278860 281299 303060 321141 328991 331063 350134 350426 368250 368735 370119 386254 388201 400199 418207 428167 436109 469186 513106 515217 526451 531079 533178 543074 550686 583354 597463 660141 662247 680271 690175 712446 715408 775341 783461 793304 826487 854470 859446 860243 862297 880381 890053 906358 933444 933698 942687 961304 979401 989633 998619 1015277 1015902 1024695 1052592 1071209 1080198 1080452 1089188 1123758 1151565 1159409 1177517 1215822 1220592 1230413 1238555 1248489 1301403 1319503 1335747 1351640 1387723 1398482 1416433 1452982 1463210 1470822 1482817 1487363 1496618 1498697 1544710 1595721 1613704 1643777 1645161 1645646 1682847 1744751 1753681 1767040 1771864 1784792 1995885 
15.0 2.402 1.361 4.481 2.165 1.02 2.137 4.839 1.291 0.739 3.071 2.961 1.733 6.213 2.256 2.354 0.302 5.749 8.053 3.658 0.598 11.766 18.115 0.416 4.744 0.805 3.95 18.535 8.194 1.5 8.424 2.912 0.834 1.153 1.346 1.952 15.809 1.859 1.003 10.549 0.049 6.063 10.249 1.822 1.174 13.4 0.773 2.207 12.27 2.89 4.501 2.551 0.642 0.517 0.135 2.033 1.336 0.774 0.006 0.426 7.891 4.206 0.495 2.483 1.925 1.362 1.267 4.535 10.501 13.2 2.405 1.396 0.612 10.052 7.327 0.237 11.874 2.599 0.817 17.275 0.747 1.848 0.62 0.951 1.445 0.093 1.486 7.618 1.305 19.577 0.389 18.4 12.814 2.186 8.894 1.054 3.34 1.586 1.089 0.071 2.922 1.771 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_1125_0.prm:15
 Score: 87.112, AlignedPeaks: 370080 526323 597376 712429 783408 854453 951460 1052781 1151601 1238614 1351694 
0 258543 258836 261809 266044 268511 276675 277985 317287 350086 350345 354085 357405 364276 366364 368158 369519 370080 386690 388434 400177 428170 469327 473045 474209 479343 492356 493069 497264 498970 508490 525835 526323 528192 583467 597376 643288 659277 712429 754255 756337 772193 774292 782384 783408 783988 784242 826404 854453 901299 903340 919461 921381 931375 951460 989134 998574 1006555 1016426 1033550 1034373 1040240 1052781 1063299 1103407 1107546 1136483 1144858 1145117 1147494 1149543 1151601 1191741 1202220 1220667 1238614 1248485 1256466 1256933 1265906 1335579 1351694 1353741 1400555 1418626 1471632 1496664 1498708 1542591 1560643 1595781 1611752 1629773 1647607 1657678 1659651 1671573 1680164 1726848 1728667 1729205 1729825 1739802 1743836 1746550 1757776 1884959 1885521 1886953 1904695 1977055 1978365 1986529 1988996 1991429 1993231 1996204 1996497 2237030 
15.0 7.837 8.683 1.242 2.131 1.64 4.497 1.107 2.35 3.017 2.958 5.914 1.78 1.632 2.681 15.508 6.732 10.072 4.438 1.935 0.548 0.133 0.947 1.306 7.069 1.558 3.517 6.916 4.694 1.184 2.317 3.735 10.547 0.549 1.192 3.317 0.363 6.116 9.218 2.328 14.723 0.019 3.021 1.868 7.762 2.782 2.782 0.409 13.033 0.707 17.67 0.182 2.216 1.416 2.18 0.096 0.498 1.55 8.853 1.307 2.781 0.889 3.356 0.003 8.367 0.504 5.742 0.378 2.564 0.96 0.208 8.12 1.641 6.261 0.167 1.383 1.776 2.712 6.788 3.24 0.368 18.124 0.22 13.771 2.385 8.498 0.823 18.853 8.571 2.303 10.213 1.341 3.348 0.291 6.39 1.593 0.082 0.554 0.57 10.783 7.62 1.117 2.7 1.183 5.168 6.192 8.12 2.214 18.243 0.238 1.329 1.902 0.705 1.399 1.371 0.751 17.508 13.224 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_975_0.prm:25
 Score: 85.191, AlignedPeaks: 1156496 1271504 1342589 1413557 1611692 1797776 1910901 
0 131255 269069 275343 281268 293507 299169 310826 325226 353254 382130 385945 395180 403129 428164 429016 500105 507851 512844 521729 558277 565023 569101 606891 613413 641264 648056 656881 658440 671490 697035 705941 713905 728025 749428 762497 771569 811310 848605 857295 891828 898875 911502 920500 925341 955595 964212 966685 971546 973084 1019560 1026376 1043364 1071669 1100724 1113442 1138830 1142284 1147912 1148692 1153166 1156496 1170426 1172745 1174729 1186378 1191752 1213589 1257352 1271504 1275557 1292376 1301762 1314519 1319621 1330379 1332429 1340702 1342589 1411521 1413557 1427575 1429603 1453566 1455647 1498580 1500699 1524662 1526690 1540708 1542715 1560726 1609727 1611692 1613563 1623886 1639746 1652503 1678708 1682761 1696913 1740682 1767887 1779536 1781520 1783839 1797776 1799955 1801099 1805573 1806353 1811981 1815435 1840823 1882596 1910901 1927889 1981181 1987580 1990053 1998670 2027495 2028924 2033765 2042763 2055389 2062437 2096969 2105660 2142955 2148250 2182696 2190867 2191768 2200650 2204837 2226240 2240360 2248324 2257230 2282775 2306279 2347374 2375785 2385164 2389242 2389896 2395988 2432536 2441421 2446414 2454160 2521487 2525249 2526101 2551122 2559085 2568320 2572135 2601011 2639083 2643439 2655096 2660758 2672997 2678922 2685196 2808159 2823010 2936254 
15.0 3.789 2.899 3.537 0.479 2.346 3.483 5.207 0.791 2.492 7.256 2.232 2.106 6.899 0.304 5.124 2.417 1.974 1.216 2.59 3.77 1.529 3.766 4.21 3.742 9.784 5.307 1.077 0.819 1.831 2.779 0.779 2.192 4.704 2.18 2.818 0.839 9.274 2.695 11.084 3.046 2.736 2.38 2.992 2.944 3.549 2.124 1.648 3.011 6.659 1.327 6.513 11.467 4.141 3.047 5.545 3.247 0.297 3.943 2.073 1.576 19.279 9.411 3.541 3.282 1.155 0.319 7.083 7.811 1.228 3.599 0.159 0.314 3.108 1.275 0.212 7.488 2.33 11.996 21.87 2.655 6.47 10.728 0.889 14.199 14.142 1.58 2.265 7.969 3.833 28.312 5.204 2.203 16.515 0.19 2.093 5.155 0.524 1.484 0.322 6.554 10.358 0.923 0.759 4.081 10.766 23.667 4.586 5.418 2.616 0.166 1.171 11.708 8.012 4.799 9.851 7.72 8.145 1.578 2.276 3.482 2.919 2.937 2.549 2.616 3.003 2.668 15.394 6.082 8.451 5.322 7.724 7.123 4.408 1.485 3.429 6.137 3.628 6.212 2.721 4.599 5.759 3.231 6.018 1.644 3.788 4.711 1.995 1.733 1.292 1.174 0.268 0.274 4.297 0.683 6.813 0.636 2.921 4.53 0.13 0.667 6.066 0.853 1.063 0.164 4.034 3.004 0.255 5.088 15.0 

SpectrumHMM Model: * M[0] - Mass:-370285.22222222213 Overlap:4/4 LogOddsScore:7.24861417052274, SumScore:48.77, InsertsAfter: 20
 * M[1] - Mass:-1926.3333333333333 Overlap:3/5 LogOddsScore:3.2351722916053958, SumScore:23.778, InsertsAfter: 61
 * M[2] - Mass:0.0 Overlap:5/7 LogOddsScore:6.760383435861036, SumScore:104.505, InsertsAfter: 2
 * M[3] - Mass:156158.1666666667 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:135.525, InsertsAfter: 68
 * M[4] - Mass:227215.15384615384 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:175.90699999999998, InsertsAfter: 26
 * M[5] - Mass:342170.07692307694 Overlap:7/7 LogOddsScore:10.467179611325355, SumScore:227.07799999999997, InsertsAfter: 26
 * M[6] - Mass:413192.8461538461 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:225.388, InsertsAfter: 19
 * M[7] - Mass:484199.92307692306 Overlap:7/7 LogOddsScore:14.099406890326001, SumScore:247.471, InsertsAfter: 20
 * M[8] - Mass:581082.5 Overlap:4/7 LogOddsScore:5.51235656129565, SumScore:183.02700000000002, InsertsAfter: 30
 * M[9] - Mass:682298.6153846155 Overlap:7/7 LogOddsScore:11.677922037658904, SumScore:245.69, InsertsAfter: 34
 * M[10] - Mass:781379.1111111111 Overlap:5/7 LogOddsScore:7.971125862194585, SumScore:250.065, InsertsAfter: 32
 * M[11] - Mass:868299.1000000001 Overlap:6/7 LogOddsScore:9.21915273675997, SumScore:514.8, InsertsAfter: 32
 * M[12] - Mass:981569.6153846155 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:542.217, InsertsAfter: 30
ConsensusPRM: -370285 -1926 0 156158 227215 342170 413192 484199 581082 682298 781379 868299 981569 Consensus: -370285 -1926 0 156158 227215 342170 413192 484199 581082 682298 781379 868299 981569
De Novo: RADAAPTVSI, Merged: RADAAPTVSIFPPSSEQITSGGASVVCFINNFYPKDINVKWKIDGSERQNGVINSWTDQDSKDSTYSMSSTITITKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
-370285 -1926 0 156158 227215 342170 413192 484199 581082 682298 781379 868299 981569 1128637 1225689 1322741 1409773 1496805 1625847 1753905 1866989 1968036 2055068 2112089 2169110 2240147 2327179 2426247 2525315 2685399 2832467 2945551 3059593 3173635 3320703 3483766 3580818 3708912 3823938 3937022 4051064 4150132 4278226 4464305 4592399 4705483 4820509 4877530 4964562 5093604 5249705 5377763 5491805 5548826 5647894 5760978 5875020 5962052 6148131 6249178 6364204 6492262 6607288 6694320 6822414 6937440 7024472 7125519 7288582 7375614 7506654 7593686 7680718 7781765 7894849 7995896 8108980 8210027 8338121 8453147 8582189 8745252 8874294 9030395 9167453 9281495 9368527 9531590 9632637 9792721 9921763 9992800 10093847 10230905 10358999 10460046 10547078 10648125 10735157 10832209 10945293 11044361 11172455 11259487 11406555 11520597 11676698 11790740 11919782 12079866 
48.77 23.778 89.7525 112.7625 155.4535 203.539 202.69400000000002 213.7355 181.51350000000002 227.845 230.0325 497.4 511.1085 480.0 480.0 480.0 480.0 480.0 525.0 480.0 525.0 735.0 645.0 750.0 750.0 765.0 765.0 735.0 750.0 855.0 1350.0 1350.0 1485.0 1500.0 1590.0 1590.0 1620.0 1710.0 1200.0 1050.0 1095.0 1035.0 1110.0 1035.0 945.0 870.0 960.0 840.0 825.0 1005.0 1095.0 1140.0 1320.0 1320.0 1320.0 1620.0 1590.0 1650.0 1770.0 1785.0 1785.0 1860.0 1950.0 1830.0 2520.0 2775.0 2475.0 2475.0 2610.0 2460.0 2505.0 2565.0 2565.0 2580.0 2595.0 2565.0 2460.0 2460.0 2460.0 1890.0 1890.0 1155.0 1170.0 1350.0 480.0 540.0 510.0 675.0 630.0 630.0 855.0 795.0 795.0 975.0 1155.0 810.0 840.0 840.0 840.0 840.0 840.0 990.0 1065.0 765.0 735.0 540.0 480.0 480.0 480.0 465.0 
(RIGHT)Round: 0 for seed: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
[0]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_600_0.prm:153
 Score: 96.21799999999999, AlignedPeaks: 0 128110 215114 362148 476237 746352 875336 
0 98874 128110 144122 211042 215114 226152 312060 324678 330079 347023 347719 362148 459125 476237 489226 498485 539203 543997 573139 578949 587562 611096 611721 620039 626505 708064 716851 724096 732852 746352 767795 776411 781479 866291 875336 893434 979302 1059341 1187444 
15.0 0.857 13.787 1.347 3.733 17.447 8.206 7.526 0.608 22.171 5.582 0.604 4.527 8.547 3.263 0.191 1.917 3.568 1.962 3.083 0.206 0.368 9.198 2.418 4.091 0.214 4.239 2.129 3.3 1.161 8.78 3.672 2.529 0.884 1.163 18.414 5.357 0.112 11.948 15.0 

[1]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_550_0.prm:414
 Score: 86.439, AlignedPeaks: 0 234120 348150 504213 618245 747250 
0 137171 234120 251096 253172 348150 354114 372112 388051 389123 487214 501146 504213 568793 577344 586091 603189 615123 618245 632194 634244 686277 694601 702346 731357 747250 754525 765327 783147 851261 884197 885290 886085 954062 964403 1101398 
15.0 1.011 28.156 26.206 20.77 3.11 6.002 19.265 1.152 5.275 2.639 9.467 4.998 1.249 2.565 0.795 0.288 6.74 3.45 0.51 0.122 3.971 0.531 1.154 0.316 16.725 0.594 3.836 0.865 1.823 2.777 2.775 8.966 0.496 0.535 15.0 

[2]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_600_0.prm:67
 Score: 82.793, AlignedPeaks: 0 234073 348148 504192 618298 747278 
0 112961 194062 212073 234073 252179 346045 348148 363062 363856 467043 484016 490579 504192 517001 538170 582117 584364 596081 597457 599289 616116 616889 618298 624466 624938 625996 676176 697344 710177 713218 723767 739261 747278 781071 789124 789736 797099 798437 810384 840584 849086 866176 868296 925349 980246 1196336 
15.0 1.71 2.419 4.116 19.873 0.332 18.717 10.992 9.172 1.925 15.978 1.487 0.192 6.004 2.374 0.023 3.642 0.842 5.492 0.485 0.52 10.003 1.206 4.055 3.438 3.281 2.55 0.459 0.005 8.929 2.807 0.036 1.236 11.869 9.361 0.987 3.472 1.666 1.167 0.125 2.616 2.459 3.952 2.541 2.384 13.338 15.0 

[3]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Trypsin_0_0_525_0.prm:85
 Score: 78.105, AlignedPeaks: 0 86820 234143 348184 504212 618233 747275 
0 86820 211126 226118 234143 330069 346051 348184 389919 391181 416205 440577 445184 459087 504212 521028 530726 547438 555612 556346 556922 564978 573094 588040 618233 636342 636784 644150 652529 653268 661156 678514 686180 703537 712156 747275 815222 843212 1059351 
15.0 5.438 9.228 0.015 15.393 21.941 2.17 0.884 0.431 0.216 1.056 4.353 2.187 11.098 6.456 3.705 1.923 4.33 0.78 8.249 2.81 0.406 7.734 1.138 5.05 10.951 5.99 4.604 2.56 1.234 6.777 1.171 0.652 1.152 4.593 14.884 1.613 5.951 15.0 

[4]:/home/natalie/Projects/MySVNProjects/ImmunoSeq/AntibodyData/aLTA/PRMs/New_02162010/LTQ/3F12_LTQ_Other_0_0_575_0.prm:123
 Score: 75.996, AlignedPeaks: 0 234078 348010 504244 618372 747298 
0 170074 183868 234078 285976 302885 348010 388778 405850 406934 423952 424786 504244 521988 531386 535838 585440 586141 594912 618372 650040 694024 720353 721081 724066 729621 732424 737136 738528 747298 765339 780481 781132 788991 807427 839071 850734 920149 1021276 1136211 
15.0 1.277 1.363 23.665 21.231 2.126 1.845 3.361 2.591 17.925 1.368 0.906 7.061 3.955 0.659 7.355 2.264 0.451 4.792 2.591 8.974 3.899 0.001 6.974 2.525 7.553 0.874 1.382 1.176 10.834 6.099 1.435 3.544 1.844 1.616 0.39 0.294 17.443 1.436 15.0 

SpectrumHMM Model: * M[0] - Mass:0.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:840.0, InsertsAfter: 0
 * M[1] - Mass:113084.0 Overlap:2/2 LogOddsScore:4.735953570589189, SumScore:840.0, InsertsAfter: 0
 * M[2] - Mass:212152.0 Overlap:3/3 LogOddsScore:6.850792719803261, SumScore:1005.0, InsertsAfter: 1
 * M[3] - Mass:340249.19999999995 Overlap:7/7 LogOddsScore:15.31014931665955, SumScore:1138.787, InsertsAfter: 2
 * M[4] - Mass:427188.4 Overlap:4/7 LogOddsScore:6.723098987629199, SumScore:787.885, InsertsAfter: 14
 * M[5] - Mass:574341.8 Overlap:7/7 LogOddsScore:14.352544526406524, SumScore:826.614, InsertsAfter: 9
 * M[6] - Mass:688386.2000000001 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:560.094, InsertsAfter: 33
 * M[7] - Mass:844461.125 Overlap:6/7 LogOddsScore:8.00841031042642, SumScore:504.519, InsertsAfter: 33
 * M[8] - Mass:958518.5 Overlap:7/7 LogOddsScore:9.256437184991807, SumScore:503.926, InsertsAfter: 38
 * M[9] - Mass:1087517.5 Overlap:7/7 LogOddsScore:12.888664463992452, SumScore:552.726, InsertsAfter: 28
 * M[10] - Mass:1247657.0 Overlap:2/7 LogOddsScore:3.0163028121648807, SumScore:465.0, InsertsAfter: 7
 * M[11] - Mass:1399596.5 Overlap:2/5 LogOddsScore:3.1978878433735596, SumScore:30.0, InsertsAfter: 3
ConsensusPRM: 0 113084 212152 340249 427188 574341 688386 844461 958518 1087517 1247657 1399596 Consensus: 0 113084 212152 340249 427188 574341 688386 844461 958518 1087517 1247657 1399596
De Novo: IVKSFNRNEC, Merged: RADAAPTVSIFPPSSEQITSGGASVVCFINNFYPKDINVKWKIDGSERQNGVINSWTDQDSKDSTYSMSSTITITKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
0 156101 227138 342164 413201 484238 581290 682337 781405 868437 981521 1128589 1225641 1322693 1409725 1496757 1625799 1753857 1866941 1967988 2055020 2112041 2169062 2240099 2327131 2426199 2525267 2685351 2832419 2945503 3059545 3173587 3320655 3483718 3580770 3708864 3823890 3936974 4051016 4150084 4278178 4464257 4592351 4705435 4820461 4877482 4964514 5093556 5249657 5377715 5491757 5548778 5647846 5760930 5874972 5962004 6148083 6249130 6364156 6492214 6607240 6694272 6822366 6937392 7024424 7125471 7288534 7375566 7506606 7593638 7680670 7781717 7894801 7995848 8108932 8209979 8338073 8453099 8582141 8745204 8874246 9030347 9167405 9281447 9368479 9531542 9632589 9792673 9921715 9992752 10093799 10230857 10358951 10459998 10547030 10648077 10735109 10832161 10945245 11044313 11172407 11259439 11406507 11520549 11676650 11790692 11919734 12079818 12231757 
75.0 90.0 135.0 180.0 180.0 180.0 180.0 210.0 210.0 480.0 480.0 480.0 480.0 480.0 480.0 480.0 525.0 480.0 525.0 735.0 645.0 750.0 750.0 765.0 765.0 735.0 750.0 855.0 1350.0 1350.0 1485.0 1500.0 1590.0 1590.0 1620.0 1710.0 1200.0 1050.0 1095.0 1035.0 1110.0 1035.0 945.0 870.0 960.0 840.0 825.0 1005.0 1095.0 1140.0 1320.0 1320.0 1320.0 1620.0 1590.0 1650.0 1770.0 1785.0 1785.0 1860.0 1950.0 1830.0 2520.0 2775.0 2475.0 2475.0 2610.0 2460.0 2505.0 2565.0 2565.0 2580.0 2595.0 2565.0 2460.0 2460.0 2460.0 1890.0 1890.0 1155.0 1170.0 1350.0 480.0 540.0 510.0 675.0 630.0 630.0 855.0 795.0 795.0 975.0 1155.0 810.0 840.0 840.0 840.0 840.0 840.0 997.5 1101.8935000000001 771.4372006188479 780.807 550.047 490.5910668729493 491.96299999999997 516.363 456.65783436474646 19.98940123769577 
# ----SEED INFO----

### Path 0 ###
# Templates 0:1.Mouse_Rat_HC.AC090843|IGHV1-9*01|Mus musculus_C57BL/6|F|V-REGION|86194..86487| seeds: 
# Template: QVQLQQSGAELMKPGASVKLSCKATGYTFTGYWIEWVKQRPGHGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAYMQLSSLTTEDSAIYYCAR
# Seed[0][0]: QSGAELMKPGASVKLSCKATGYTFTGYWIEWVKQRPGHGLEWIGE -> [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISPGSGSTNYNEEFQ
  [0]: VKLSCKATGYTF
  [1]: VKLSCKATGYTF
  [2]: LMKPGASVKLS
  [3]: QSGAELMKPGASV
  [4]: SGAELMKPGASV
  [5]: GAELMKPGASVK
  [6]: SGAELMKPGASVK
  [7]: QSGAELMKPGASV
  [8]: ATGYTFTGG->WYWIEWVK
  [9]: WIEWVKQRPGHGL
  [10]: WIEWVKQRPGHGL
  [11]: WIEWVKQRPGHGLEWIG
  [12]: WVKQRPGHGLEW
  [13]: WVKQRPGHGLEW
  [14]: WIEWVKQRPGHG
  [15]: WIEWVKQRPGHG
  [16]: WIEWVKQRPGHGLE
  [17]: WIEWVKQRPGHGLE
  [18]: WVKQRPGHGLEWIGE
  [19]: WVKQRPGHGLEWIGE
  [20]: IEWVKQRPGHGLEWIG
  [21]: VKQRPGHGLE
  [22]: VKQRPGHGLE
  [23]: VKQRPGHGLE
  [24]: IEWVKQRPGHGLEWIGE
  [25]: WIEWVKQRPGHGLEWIGE
  [26]: IEWVKQRPGHGLEW
  [27]: IEWVKQRPGHGLEW
  [28]: IEWVKQRPGHGL
  [29]: WVKQRPGHGLEWIG
  [30]: WIEWVKQRPGHGLEW
  [31]: WIEWVKQRPGHGLEW
  [32]: QRPGHGLE
  [33]: YWIEWVK
  [34]: IEWVKQRPGHGLE
  [35]: YWIEWVK
  [36]: WVKQRPGHGLE
  [37]: ASVKLSCKATGYTFTGG->YYWIEWVK
  [38]: SGAELMKPGASVK
  Peptides: QRPGHGLE,SGAELMKPGASVK,WIEWVKQRPGHG,IEWVKQRPGHGLE,WVKQRPGHGLE,ATGYTFTGYWIEWVK,IEWVKQRPGHGL,QSGAELMKPGASV,VKQRPGHGLE,WIEWVKQRPGHGLE,GAELMKPGASVK,ASVKLSCKATGYTFTGYWIEWVK,IEWVKQRPGHGLEWIG,SGAELMKPGASV,WVKQRPGHGLEWIGE,WIEWVKQRPGHGL,LMKPGASVKLS,IEWVKQRPGHGLEWIGE,WIEWVKQRPGHGLEWIGE,WVKQRPGHGLEWIG,VKLSCKATGYTF,IEWVKQRPGHGLEW,WIEWVKQRPGHGLEW,WVKQRPGHGLEW,WIEWVKQRPGHGLEWIG,YWIEWVK
  Total Peptides: 26
# Seed[0][1]: NEKFKGKATFTADTSSN -> [316.128]IWNEQFKGKATFTADTSSNQAYIQISSIT[216.095]
  [0]: NEKFKGKATF
  [1]: FKGKATFTADTT->WSSN
  Peptides: FKGKATFTADTSSN,NEKFKGKATF
  Total Peptides: 2
# Templates 3:4.Mouse_Rat_HC.V00801|IGHG2B*02|Mus musculus|F|CH1+H+CH2+CH3+CH-S|134..424+741.. seeds: 
# Template: AKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPNLEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMKTSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK
# Seed[3][0]: AKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPNLEGGPSVFIFPPNIKDVLMISLTPKVTC -> [200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC
  [0]: TTGSSVTLGCLVK
  [1]: TTGSSVTLGCLVK
  [2]: TTPPSVYPLAPGCGDTTGSSVTLGCLVK
  [3]: TTPPSVYPLAPGCGDTTGSSVTLGCLVK
  [4]: TTPPSVYPLAPGCGDTTGSSVTLGCLVK
  [5]: TTPPSVYPLAPGCGDTTGSSVTLGCLVK
  [6]: TTPPSVYPLAPGCGDTTGSSVTLGCLVK
  [7]: GCLVKGYFPESVTVTW
  [8]: SVTVTWNSGSLSSSVHTFPALL
  [9]: SVTVTWNSGSLSSSVHTFPALL
  [10]: SVTVTWNSGSLSSSVHTFPALL
  [11]: VTWNSGSLSSSVHTF
  [12]: VTWNSGSLSSSVHTF
  [13]: VTWNSGSLSSSVHTF
  [14]: VTWNSGSLSSSVHTF
  [15]: VTWNSGSLSSSVHTF
  [16]: VTWNSGSLSSSVHTF
  [17]: VTWNSGSLSSSVHTF
  [18]: VTWNSGSLSSSVHTF
  [19]: VTWNSGSLSSSVHTF
  [20]: VTWNSGSLSSSVHTF
  [21]: VTWNSGSLSSSVHTF
  [22]: VTWNSGSLSSSVHTF
  [23]: VTVTWNSGSLSSSVHTFPAL
  [24]: VTVTWNSGSLSSSVHTFPAL
  [25]: SVTVTWNSGSLSSSVHTFPALLQ
  [26]: SVTVTWNSGSLSSSVHTFPALLQ
  [27]: SVTVTWNSGSLSSSVHTFPALLQ
  [28]: SVTVTWNSGSLSSSVHTFPALLQ
  [29]: VTVTWNSGSLSSSVHTF
  [30]: TVTWNSGSLSSSVHTFPAL
  [31]: TVTWNSGSLSSSVHTFPAL
  [32]: TVTWNSGSLSSSVHTFPAL
  [33]: WNSGSLSSSVHTFPALLQ
  [34]: WNSGSLSSSVHTFPALLQ
  [35]: NSGSLSSSVHTFPALLQ
  [36]: NSGSLSSSVHTFPALLQ
  [37]: NSGSLSSSVHTFPALLQ
  [38]: NSGSLSSSVHTFPALLQ
  [39]: VTWNSGSLSSSVHTFPAL
  [40]: VTWNSGSLSSSVHTFPAL
  [41]: VTWNSGSLSSSVHTFPAL
  [42]: VTWNSGSLSSSVHTFPAL
  [43]: VTWNSGSLSSSVHTFPAL
  [44]: VTWNSGSLSSSVHTFPAL
  [45]: TWNSGSLSSSVHTFPAL
  [46]: TVTWNSGSLSSSVHTF
  [47]: TVTWNSGSLSSSVHTF
  [48]: SVTVTWNSGSLSSSVHTFPALLQSG
  [49]: WNSGSLSSSVHTFPAL
  [50]: WNSGSLSSSVHTFPAL
  [51]: SVTVTWNSGSLSSSVHT
  [52]: VTWNSGSLSSSVHTFPALLQ
  [53]: VTWNSGSLSSSVHT
  [54]: VTVTWNSGSLSS
  [55]: NSGSLSSSVHTFPAL
  [56]: WNSGSLSSSVHTFPALL
  [57]: WNSGSLSSSVHTFPALL
  [58]: VTWNSGSLSSSVHTFPALL
  [59]: VTWNSGSLSSSVHTFPALL
  [60]: VTWNSGSLSSSVHTFPALL
  [61]: VTWNSGSLSSSVHTFPALL
  [62]: TWNSGSLSSSVHTF
  [63]: NSGSLSSSVHTFPALLQSGLY
  [64]: NSGSLSSSVHTFPALLQSGLY
  [65]: NSGSLSSSVHTFPALLQSGLY
  [66]: NSGSLSSSVHTFPALLQSGLY
  [67]: NSGSLSSSVHTFPALLQSGLY
  [68]: SGSLSSSVHTFPALL
  [69]: SGSLSSSVHTFPALL
  [70]: SGSLSSSVHTFPALL
  [71]: SGSLSSSVHTFPALL
  [72]: KTTPPSVYPLAPGCGDTTGSSVTLGCLV
  [73]: AKTTPPSVYPLAPGCGDTTGSS
  [74]: NSGSLSSSVH
  [75]: NSGSLSSSVH
  [76]: NSGSLSSSVH
  [77]: NSGSLSSSVH
  [78]: NSGSLSSSVH
  [79]: SVTVTWNSGSLSSSVH
  [80]: SVTVTWNSGSLSSSVH
  [81]: VTWNSGSLSSS
  [82]: TVTWNSGSLSSSVHTFPALL
  [83]: TFPALLQSGLY
  [84]: TFPALLQSGLY
  [85]: TFPALLQSGLY
  [86]: TFPALLQSGLY
  [87]: VTWNSGSLSS
  [88]: VTWNSGSLSS
  [89]: SGSLSSSVHTFPALLQ
  [90]: SGSLSSSVHTFPALLQ
  [91]: SGSLSSSVHTFPALLQ
  [92]: SGSLSSSVHTFPALLQ
  [93]: SGSLSSSVHTFPALLQ
  [94]: SGSLSSSVHTFPALLQ
  [95]: SGSLSSSVHTFPALLQ
  [96]: NSGSLSSSVHTFPALL
  [97]: NSGSLSSSVHTFPALL
  [98]: NSGSLSSSVHTFPALL
  [99]: GYFPESVTVT
  [100]: GYFPESVTVT
  [101]: GYFPESVTVT
  [102]: SVTVTWNSGSLS
  [103]: SSVTLGCLVK
  [104]: SSVTLGCLVK
  [105]: SSVTLGCLVK
  [106]: SSVTLGCLVK
  [107]: SSSVHTFPALLQSGLY
  [108]: SSVHTFPALLQSGLYT
  [109]: KTTPPSVYPLAPGCGDTTGSS
  [110]: KTTPPSVYPLAPGCGDTTGSS
  [111]: TMSSSVTVPSSTWPSQTVTC
  [112]: VTVPSSTWPSQ
  [113]: SGSLSSSVHTFPAL
  [114]: SGSLSSSVHTFPAL
  [115]: VTVPSSTWPSQTVTCS
  [116]: KLEPSGPISTINPCPPCK
  [117]: KLEPSGPISTINPCPPCK
  [118]: KLEPSGPISTINPCPPCK
  [119]: KLEPSGPISTINPCPPCK
  [120]: KLEPSGPISTINPCPPCK
  [121]: KLEPSGPISTINPCPPCK
  [122]: KLEPSGPISTINPCPPCK
  [123]: KLEPSGPISTINPCPPCK
  [124]: KLEPSGPISTINPCPPCK
  [125]: KLEPSGPISTINPCPPCK
  [126]: KLEPSGPISTINPCPPCK
  [127]: KLEPSGPISTINPCPPCK
  [128]: LEPSGPISTINPCPPCK
  [129]: LEPSGPISTINPCPPCK
  [130]: LEPSGPISTINPCPPCK
  [131]: LEPSGPISTINPCPPCK
  [132]: LEPSGPISTINPCPPCK
  [133]: LEPSGPISTINPCPPCK
  [134]: LEPSGPISTINPCPPCK
  [135]: LEPSGPISTINPCPPCK
  [136]: LEPSGPISTINPCPPCKE
  [137]: LEPSGPISTINPCPPCKE
  [138]: LEPSGPISTINPCPPCKEC
  [139]: LEPSGPISTINPCPPCKEC
  [140]: PSGPISTINPCPPCKE
  [141]: PSGPISTINPCPPCKE
  [142]: PSGPISTINPCPPCKE
  [143]: PSGPISTINPCPPCKE
  [144]: PSGPISTINPCPPCKE
  [145]: SVAHPASSTTVDKK
  [146]: SVAHPASSTTVDKK
  [147]: SVAHPASSTTVDKK
  [148]: SVAHPASSTTVDKKLE
  [149]: KLEPSGPISTINPCPPCKECH
  [150]: KLEPSGPISTINPCPPCKECH
  [151]: KLEPSGPISTINPCPPCKECH
  [152]: KLEPSGPISTINPCPPCKECH
  [153]: KLEPSGPISTINPCPPCKECH
  [154]: KLEPSGPISTINPCPPCKE
  [155]: KLEPSGPISTINPCPPCKE
  [156]: KLEPSGPISTINPCPPCKE
  [157]: SGPISTINPCPPCKE
  [158]: SGPISTINPCPPCKE
  [159]: SVAHPASSTTVDK
  [160]: SVAHPASSTTVDK
  [161]: SVAHPASSTTVDK
  [162]: SVAHPASSTTVDK
  [163]: PSGPISTINPCPPCK
  [164]: PSGPISTINPCPPCK
  [165]: GPISTINPCPPCKE
  [166]: GPISTINPCPPCKE
  [167]: KLEPSGPIST
  [168]: KLEPSGPIST
  [169]: KLEPSGPIST
  [170]: NPCPPCKECH
  [171]: STINPCPPCKECH
  [172]: STINPCPPCKECH
  [173]: STINPCPPCKECH
  [174]: KLEPSGPISTINPCPPC
  [175]: KLEPSGPISTINPCPPC
  [176]: KLEPSGPISTINPCPPC
  [177]: KLEPSGPISTINPCPPC
  [178]: KLEPSGPISTINPCPPC
  [179]: KLEPSGPISTINPCPPC
  [180]: KLEPSGPISTINPCPPC
  [181]: KLEPSGPISTINPCPPC
  [182]: VAHPASSTTVDKKLE
  [183]: KLEPSGPISTIN
  [184]: KLEPSGPISTIN
  [185]: KLEPSGPISTIN
  [186]: KLEPSGPISTIN
  [187]: KLEPSGPISTIN
  [188]: KLEPSGPISTIN
  [189]: VTWNSGSLS
  [190]: KKLEPSGPISTINPCPPCKECH
  [191]: KLEPSGPISTINPCPPCKECHK
  [192]: CPAPNLEGGPSVFIFPPNIK
  [193]: CPAPNLEGGPSVFIFPPNIK
  [194]: CPAPNLEGGPSVFIFPPNIK
  [195]: CPAPNLEGGPSVFIFPPNIK
  [196]: CPAPNLEGGPSVFIFPPNIK
  [197]: CPAPNLEGGPSVFIFPPNIK
  [198]: CPAPNLEGGPSVFIFPPNIK
  [199]: CPAPNLEGGPSVFIFPPNIK
  [200]: CPAPNLEGGPSVFIFPPNIK
  [201]: KCPAPNLEGGPSVF
  [202]: IFPPNIKDVLMISLTPK
  [203]: IFPPNIKDVLMISLTPK
  [204]: IFPPNIKDVLMISLTPK
  [205]: IFPPNIKDVLMISLTPK
  [206]: GGPSVFIFPPNIKD
  [207]: GGPSVFIFPPNIKD
  [208]: GGPSVFIFPPNIKD
  [209]: GGPSVFIFPPNIKD
  [210]: DVLMISLTPK
  [211]: DVLMISLTPK
  [212]: DVLMISLTPK
  [213]: DVLMISLTPK
  [214]: DVLMISLTPK
  [215]: CPAPNLEGGPSVFIFPPNIKDVLMISLTPK
  [216]: CPAPNLEGGPSVFIFPPNIKDVLMISLTPK
  [217]: CPAPNLEGGPSVFIFPPNIKDVLMISLTPK
  [218]: CPAPNLEGGPSVFIFPPNIKDVLMISLTPK
  [219]: KLEPSGPISTINPCPPCKECHK
  [220]: KLEPSGPISTINPCPPCKECHK
  [221]: KLEPSGPISTINPCPPCKECHK
  [222]: KLEPSGPISTINPCPPCKECHK
  [223]: KLEPSGPISTINPCPPCKECHK
  [224]: KCPAPNLEGGPSVFIFPPNI
  [225]: KCPAPNLEGGPSVFIFPPNI
  [226]: KCPAPNLEGGPSVFIFPPNI
  [227]: KCPAPNLEGGPSVFIFPPNI
  [228]: KCPAPNLEGGPSVFIFPPNI
  [229]: KCPAPNLEGGPSVFIFPPNI
  [230]: KCPAPNLEGGPSV
  [231]: HPASSTTVDKKLE
  [232]: HPASSTTVDKKLE
  [233]: KLEPSGPISTINPCPPCKEC
  [234]: KLEPSGPISTINPCPPCKEC
  [235]: KTTPPSVYPLAPGCGDTTGSSVTL
  [236]: VKGYFPESVTVTW
  [237]: VKGYFPESVTVTW
  [238]: PCPPCKECHK
  [239]: ISLTPKVTC
  [240]: ISLTPKVTC
  [241]: CSVAHPASST
  [242]: CSVAHPASSTT
  [243]: TTGSSVTLGCLVKGYFPE
  [244]: SGSLSSSVHTFPALLQSGLY
  [245]: SVAHPASSTTVD
  [246]: KGYFPESVTVTWNSGSLS
  [247]: CSVAHPASSTTVDK
  [248]: CSVAHPASSTTVDK
  [249]: CSVAHPASSTTVDK
  [250]: SGLYTMSSSVTVPSSTWPSQ
  [251]: LEPSGPISTINPCPPCKECHK
  [252]: LEPSGPISTINPCPPCKECHK
  [253]: LEPSGPISTINPCPPCKECHK
  [254]: INPCPPCKECHK
  [255]: LVKGYFPESVT
  [256]: LVKGYFPESVT
  [257]: DTTGSSVTLGCLVK
  [258]: SVHTFPALLQSGLY
  [259]: TVTWNSGSLSSSVHT
  [260]: SSVHTFPALLQSGLYTMS
  [261]: SGLYTMSSSVT
  [262]: AKTTPPSVYPLAPGCGD
  [263]: ASSTTVDKKLE
  [264]: LEPSGPISTIN
  [265]: LEPSGPISTIN
  [266]: VKGYFPES
  [267]: VKGYFPES
  [268]: SGSLSSSVHTFPALLQSGLYTMS
  [269]: SLSSSVHTFPALLQ
  [270]: SLSSSVHTFPALLQ
  [271]: VKGYFPESVT
  [272]: VKGYFPESVT
  [273]: FIFPPNIKDVL
  [274]: VTVPSSTWPSQT
  [275]: SGSLSSSVHTFPALLQSG
  [276]: SGSLSSSVHTFPALLQSG
  [277]: SLSSSVHTFPALLQSGLY
  [278]: CPAPNLEGGPSV
  [279]: SGSLSSSVHTFPALLQSGL
  [280]: KTTPPSVYPLAPGCGDTTG
  [281]: PPNIKDVL
  [282]: KGYFPESVTVTWN
  [283]: VHTFPALLQ
  [284]: VKGYFPESV
  [285]: VKGYFPESV
  [286]: VTVTWNSGSL
  [287]: SSVHTFPALLQSGLYTM
  [288]: LGCLVKGYFPE
  [289]: SVTLGCLVK
  [290]: SVTLGCLVK
  [291]: FPESVTVTWN
  [292]: FPESVTVTWN
  [293]: GCLVKGYFPESVT
  [294]: IFPPNIKDVL
  [295]: SLSSSVHTFPAL
  [296]: SSVHTFPALLQ
  [297]: SSVHTFPALLQ
  [298]: SSVHTFPALLQ
  [299]: TTPPSVYPLAPGC
  [300]: KKLEPSGPISTINPCPPC
  [301]: PPCKECHK
  [302]: TMSSSVTVPSSTWPSQTVT
  [303]: SLSSSVHTFPALL
  [304]: SLSSSVHTFPALL
  [305]: KKLEPSGPISTINPCPPCKE
  [306]: KKLEPSGPISTINPCPPCKE
  [307]: GCLVKGYFPESV
  [308]: LEPSGPIST
  [309]: GSLSSSVHTFPALLQ
  [310]: GSLSSSVHTFPALLQ
  [311]: FIFPPNIKD
  [312]: FIFPPNIKD
  [313]: TWNSGSLSSSVHT
  [314]: TWNSGSLSSSVHT
  [315]: TWNSGSLSSSVHT
  [316]: VAHPASSTTVD
  [317]: TINPCPPCKE
  [318]: VAHPASSTTVDK
  [319]: TTPPSVYPLAPGCGDTTG
  [320]: PPCKECHKCPAPNL
  [321]: LVKGYFPESV
  [322]: SGLYTMSSSVTVPSSTWPSQTV
  [323]: PCPPCKE
  [324]: IFPPNIKDVLM
  [325]: SSSVHTFPALLQ
  [326]: SVTVPSSTWPSQT
  [327]: SSVHTFPALL
  [328]: SSSVHTFPAL
  [329]: SSSVHTFPAL
  [330]: GYFPESVT
  [331]: VTLGCLVKGYFPESVT
  [332]: SSSVHTFPALL
  [333]: LVKGYFPES
  [334]: FPESVTVTW
  [335]: SSVHTFPALLQSGLYTMS
  [336]: SGLYTMSSSVTVPSSTWPSS->QQ
  [337]: KLEPSGPISTIN
  [338]: TGSSVTLGCLVK
  [339]: SS->WVTVTWNSGSLSSSVHTFPALLQ
  [340]: CPAPNLEGGPSVF
  [341]: VTWNSGSLSSSVHTFPAL
  [342]: LEPSGPISTINPCPPCK
  [343]: ISLTPKVTC
  [344]: DKKLEPSGPISTINPCPPCK
  [345]: DVLMISLTPK
  [346]: VTWNSGSLSSSVHTFPAL
  [347]: PCPPCKECHK
  [348]: KLEPSGPIST
  [349]: PCPPCKECHK
  [350]: VTWNSGSLSSSVHTF
  [351]: VTWNSGSLSSSVHTFPAL
  [352]: SVAHPASSTTVDKK
  [353]: KLEPSGPIST
  [354]: IFPPNIKDVLM
  [355]: TTVDKKLEPSGPISTINPCPPCK
  [356]: SSSVTVPSSTWPSQTVTC
  [357]: SGLYTMSSSVTVPSSTWP
  [358]: SSVHTFPALLQSGLYT
  [359]: SGSLSSSVH
  [360]: KLEPSGPISTINPCPPCKECHK
  [361]: IFPPNIKDVLM
  [362]: KLEPSGPIST
  [363]: KTTPPSVYPLAPGCGDTTG
  [364]: KKLEPSGPISTIN
  [365]: SLSSSVHTFPALL
  [366]: SVAHPASSTTVDK
  [367]: SVFIFPPNIKD
  [368]: SGLYTMSSSVTVPSSTWP
  [369]: TWNSGSLSSSVHTFPALL
  [370]: MISLTPKVT
  [371]: CPAPNLEGGPSVFIFPPNIK
  [372]: PCPPCKECH
  [373]: TVTWNSGSLSSSVHT
  [374]: TTPPSVYPLAPGCGDT
  [375]: TTPPSVYPLAPGCGDT
  [376]: VTWNSGSL
  [377]: SGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDK
  [378]: SLSSSVHTFPALL
  [379]: TTPPSVYPLAPG
  [380]: LSSSVHTFPALLQ
  [381]: IFPPNIKDVL
  [382]: KLEPSGPISTINPCPPCK
  [383]: VTWNSGSLSSSV
  [384]: QSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDK
  [385]: KLEPSGPISTINPCPPCKE
  [386]: KLEPSGPISTINPCPPCKECHKCPAP
  [387]: QSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDK
  [388]: SVTVTWNSGSLSSSVHTFPALLQ
  [389]: SVTVTWN
  [390]: SVTVTWNSGSLSSSVHTFPALLQ
  Peptides: LSSSVHTFPALLQ,CSVAHPASST,LGCLVKGYFPE,SLSSSVHTFPAL,FPESVTVTWN,VTVPSSTWPSQTVTCS,KLEPSGPISTIN,TWNSGSLSSSVHTF,CPAPNLEGGPSVF,HPASSTTVDKKLE,VTWNSGSLSS,VKGYFPES,SSVHTFPALLQSGLYT,SGLYTMSSSVT,TWNSGSLSSSVHTFPALL,TTPPSVYPLAPGCGDT,MISLTPKVT,NSGSLSSSVH,VTVPSSTWPSQ,KTTPPSVYPLAPGCGDTTG,DTTGSSVTLGCLVK,VTWNSGSLSSS,SLSSSVHTFPALL,SVAHPASSTTVDKK,VKGYFPESVTVTW,WNSGSLSSSVHTFPALLQ,SGSLSSSVHTFPALLQ,VTLGCLVKGYFPESVT,SSSVHTFPAL,TVTWNSGSLSSSVHT,PSGPISTINPCPPCK,NSGSLSSSVHTFPALLQSGLY,AKTTPPSVYPLAPGCGDTTGSS,SGSLSSSVHTFPALLQSGL,VTVTWNSGSL,CPAPNLEGGPSVFIFPPNIK,TTPPSVYPLAPGCGDTTG,IFPPNIKDVLM,PPNIKDVL,IFPPNIKDVLMISLTPK,TTVDKKLEPSGPISTINPCPPCK,LVKGYFPESVT,SVTVTWN,LEPSGPISTINPCPPCKEC,VTWNSGSLSSSVHTFPAL,SGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDK,PPCKECHK,KLEPSGPISTINPCPPCKE,SGSLSSSVH,KTTPPSVYPLAPGCGDTTGSS,SVTVTWNSGSLSSSVHTFPALLQSG,SVTLGCLVK,KKLEPSGPISTINPCPPC,LEPSGPIST,SGSLSSSVHTFPAL,KKLEPSGPISTINPCPPCKECH,IFPPNIKDVL,LEPSGPISTIN,SSVHTFPALL,VTWNSGSLSSSVHTFPALLQ,VKGYFPESVT,KCPAPNLEGGPSV,VHTFPALLQ,PPCKECHKCPAPNL,GCLVKGYFPESV,KCPAPNLEGGPSVF,VTWNSGSL,GYFPESVT,TGSSVTLGCLVK,GCLVKGYFPESVT,NPCPPCKECH,GYFPESVTVT,LEPSGPISTINPCPPCKE,CSVAHPASSTT,DVLMISLTPK,SVAHPASSTTVD,ASSTTVDKKLE,SSVHTFPALLQSGLYTM,VKGYFPESV,AKTTPPSVYPLAPGCGD,VTVTWNSGSLSSSVHTFPAL,KTTPPSVYPLAPGCGDTTGSSVTL,VAHPASSTTVDK,VAHPASSTTVD,TINPCPPCKE,SSSVHTFPALLQSGLY,SLSSSVHTFPALLQSGLY,VTVTWNSGSLSSSVHTF,SSVTLGCLVK,KLEPSGPISTINPCPPCKECHK,SVAHPASSTTVDKKLE,NSGSLSSSVHTFPALLQ,QSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDK,SVTVTWNSGSLSSSVHTFPALL,NSGSLSSSVHTFPAL,TTPPSVYPLAPGC,TFPALLQSGLY,CPAPNLEGGPSV,LEPSGPISTINPCPPCK,KLEPSGPISTINPCPPCKEC,SGSLSSSVHTFPALLQSGLY,KKLEPSGPISTINPCPPCKE,GGPSVFIFPPNIKD,SGLYTMSSSVTVPSSTWPSQTV,CSVAHPASSTTVDK,CPAPNLEGGPSVFIFPPNIKDVLMISLTPK,SVTVTWNSGSLSSSVHTFPALLQ,VTWNSGSLSSSVHTFPALL,TMSSSVTVPSSTWPSQTVTC,GSLSSSVHTFPALLQ,ISLTPKVTC,SGLYTMSSSVTVPSSTWPSQ,KTTPPSVYPLAPGCGDTTGSSVTLGCLV,PCPPCKECH,KGYFPESVTVTWNSGSLS,SGSLSSSVHTFPALL,STINPCPPCKECH,SVFIFPPNIKD,SVTVTWNSGSLSSSVHT,VTVTWNSGSLSS,KLEPSGPISTINPCPPCKECH,TMSSSVTVPSSTWPSQTVT,TVTWNSGSLSSSVHTFPALL,GCLVKGYFPESVTVTW,SGPISTINPCPPCKE,SVTVTWNSGSLS,DKKLEPSGPISTINPCPPCK,FIFPPNIKD,TWNSGSLSSSVHTFPAL,GPISTINPCPPCKE,SVAHPASSTTVDK,VTVPSSTWPSQT,SLSSSVHTFPALLQ,KLEPSGPIST,FIFPPNIKDVL,VTWNSGSLSSSV,WNSGSLSSSVHTFPAL,TTPPSVYPLAPGCGDTTGSSVTLGCLVK,TTGSSVTLGCLVKGYFPE,SSSVHTFPALL,SSSVTVPSSTWPSQTVTC,WNSGSLSSSVHTFPALL,SGSLSSSVHTFPALLQSG,LVKGYFPES,SSVHTFPALLQSGLYTMS,LEPSGPISTINPCPPCKECHK,VTWNSGSLS,SVTVTWNSGSLSSSVH,KLEPSGPISTINPCPPCK,TWNSGSLSSSVHT,KGYFPESVTVTWN,TTGSSVTLGCLVK,FPESVTVTW,SGSLSSSVHTFPALLQSGLYTMS,PSGPISTINPCPPCKE,VTWNSGSLSSSVHT,SGLYTMSSSVTVPSSTWP,KKLEPSGPISTIN,SSSVHTFPALLQ,KLEPSGPISTINPCPPCKECHKCPAP,PCPPCKE,TVTWNSGSLSSSVHTF,VAHPASSTTVDKKLE,TTPPSVYPLAPG,KCPAPNLEGGPSVFIFPPNI,PCPPCKECHK,LVKGYFPESV,NSGSLSSSVHTFPALL,SVTVPSSTWPSQT,INPCPPCKECHK,SVHTFPALLQSGLY,SSVHTFPALLQ,TVTWNSGSLSSSVHTFPAL,KLEPSGPISTINPCPPC,VTWNSGSLSSSVHTF
  Total Peptides: 175
# Seed[3][1]: VVDVSEDDPDVQ -> VVDVSEDDPDVQ[351.139]
  [0]: VVDVSEDDPDVQ
  Peptides: VVDVSEDDPDVQ
  Total Peptides: 1
# Seed[3][2]: FVNNVEVHTAQTQTHRE -> FVNNVEVHTAQTQTHRE
  [0]: VHTAQTQTHRE
  [1]: VHTAQTQTHRE
  [2]: VHTAQTQTHRE
  [3]: VHTAQTQTHRE
  [4]: VHTAQTQTHRE
  [5]: FVNNVEVHT
  [6]: FVNNVEVHT
  [7]: VNNVEVH
  [8]: VNNVEVH
  Peptides: FVNNVEVHT,VNNVEVH,VHTAQTQTHRE
  Total Peptides: 3
# Seed[3][3]: RVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSL -> RVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSL
  [0]: VVSTLPIQHQDWMSGK
  [1]: VVSTLPIQHQDWMSGK
  [2]: VVSTLPIQHQDWMSGK
  [3]: VVSTLPIQHQDWMSGK
  [4]: VVSTLPIQHQDWMSGK
  [5]: VSTLPIQHQDWMSGKE
  [6]: STLPIQHQDWMSGK
  [7]: TLPIQHQDWMSGKE
  [8]: PIQHQDWMSGKEFK
  [9]: VVSTLPIQHQDW
  [10]: VVSTLPIQHQDW
  [11]: VVSTLPIQHQDW
  [12]: VVSTLPIQHQDW
  [13]: PIQHQDWMSGKE
  [14]: PIQHQDWMSGKE
  [15]: VVSTLPIQHQDWMSGKEFK
  [16]: VVSTLPIQHQDWMSGKEFK
  [17]: VVSTLPIQHQDWMSGKEFK
  [18]: VVSTLPIQHQD
  [19]: VVSTLPIQHQDWM
  [20]: VVSTLPIQHQDWM
  [21]: VSTLPIQHQDW
  [22]: VSTLPIQHQDW
  [23]: VSTLPIQHQDW
  [24]: VVSTLPIQHQ
  [25]: LPIQHQDWMSGKE
  [26]: VVSTLPIQHQDWMSG
  [27]: VVSTLPIQHQDWMSG
  [28]: VVSTLPIQHQDWMSG
  [29]: RVVSTLPIQHQDWMSGKE
  [30]: PIQHQDWMS
  [31]: STLPIQHQDW
  [32]: LPIQHQDW
  [33]: LPIQHQDW
  [34]: TLPIQHQDW
  [35]: LPIQHQDWMSGKE
  [36]: LPIQHQDWM
  [37]: LPIQHQDWM
  [38]: STLPIQHQDWMSGKE
  [39]: DWMSGKEF
  [40]: PIQHQDWMSG
  [41]: PIQHQDWMSGKE
  [42]: VVSTLPIQHQD
  [43]: FKCKVNNKDLPSPIE
  [44]: VNNKDLPSPIER
  [45]: VNNKDLPSPIER
  [46]: VNNKDLPSPIER
  [47]: VNNKDLPSPIER
  [48]: VNNKDLPSPIER
  [49]: VNNKDLPSPIER
  [50]: VNNKDLPSPIER
  [51]: VNNKDLPSPIER
  [52]: DLPSPIERTISK
  [53]: ISKIKGLVRAPQV
  [54]: APQVYILPPPAEQLSR
  [55]: APQVYILPPPAEQLSR
  [56]: APQVYILPPPAEQLSR
  [57]: APQVYILPPPAEQLSR
  [58]: APQVYILPPPAEQLSR
  [59]: APQVYILPPPAEQLSR
  [60]: APQVYILPPPAEQLSR
  [61]: APQVYILPPPAEQLSR
  [62]: LVRAPQVYILPPPAEQL
  [63]: LVRAPQVYILPPPAEQL
  [64]: ISKIKGLVRAPQV
  [65]: DLPSPIER
  [66]: DLPSPIER
  [67]: YILPPPAEQL
  [68]: YILPPPAEQL
  [69]: YILPPPAEQL
  [70]: YILPPPAEQLSRKDVSL
  [71]: IKGLVRAPQV
  [72]: YILPPPAEQ
  [73]: YILPPPAEQ
  [74]: APQVYILPPPAEQLS
  [75]: KVNNKDLPSPIERTIS
  [76]: KVNNKDLPSPIERTIS
  [77]: KVNNKDLPSPIERTIS
  [78]: NKDLPSPIE
  [79]: NKDLPSPIE
  [80]: IERTISKIKGLVRAPQV
  [81]: PSPIERTISK
  [82]: ILPPPAEQ
  [83]: LVRAPQVY
  [84]: KDLPSPIERTIS
  [85]: KDLPSPIERTIS
  [86]: ILPPPAEQL
  [87]: GLVRAPQVY
  [88]: NKDLPSPIERTISK
  [89]: VNNKDLPSPIERTISK
  [90]: CKVNNKDLPSPIER
  [91]: ILPPPAEQLS
  [92]: GLVRAPQVYILPPPAEQLSR
  [93]: DLPSPIERTIS
  [94]: CKK->PVNNKDLPSPIER
  [95]: DLPSPIERTISKIK
  [96]: RTISKIKGLVRAPQVY
  [97]: RTISKIKGLVRAPQVY
  [98]: KDLPSPIE
  [99]: ILPP->QPPAEQLSR
  [100]: VVSTLPIQHQDWMSGKE
  Peptides: NKDLPSPIERTISK,APQVYILPPPAEQLSR,CKVNNKDLPSPIER,DLPSPIER,ILPPPAEQL,LPIQHQDWM,RVVSTLPIQHQDWMSGKE,STLPIQHQDWMSGK,YILPPPAEQ,LVRAPQVY,VVSTLPIQHQDWMSGKE,ILPPPAEQ,DLPSPIERTIS,VSTLPIQHQDW,GLVRAPQVYILPPPAEQLSR,VVSTLPIQHQDWMSG,ILPPPAEQLSR,VVSTLPIQHQDWMSGK,PIQHQDWMSG,VNNKDLPSPIERTISK,GLVRAPQVY,VVSTLPIQHQDWM,VSTLPIQHQDWMSGKE,PIQHQDWMSGKE,FKCKVNNKDLPSPIE,ISKIKGLVRAPQV,TLPIQHQDW,YILPPPAEQLSRKDVSL,DLPSPIERTISK,YILPPPAEQL,VVSTLPIQHQD,VVSTLPIQHQDW,KDLPSPIE,VNNKDLPSPIER,KDLPSPIERTIS,DLPSPIERTISKIK,LPIQHQDW,PSPIERTISK,LPIQHQDWMSGKE,STLPIQHQDW,STLPIQHQDWMSGKE,VVSTLPIQHQ,ILPPPAEQLS,DWMSGKEF,IERTISKIKGLVRAPQV,PIQHQDWMS,APQVYILPPPAEQLS,NKDLPSPIE,RTISKIKGLVRAPQVY,VVSTLPIQHQDWMSGKEFK,IKGLVRAPQV,KVNNKDLPSPIERTIS,LVRAPQVYILPPPAEQL,PIQHQDWMSGKEFK,TLPIQHQDWMSGKE
  Total Peptides: 55
# Seed[3][4]: VVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMKTSKWEKTDSFSCNV -> VVGFNPGDISVEWTSNGHTEENYKDTAPVIDSDGSYFIYSKINMKTSKWEKTDSFSCNVV
  [0]: VVGFNPGDISV
  [1]: VVGFNPGDISV
  [2]: VVGFNPGDISVE
  [3]: DTAPVLDSDGSYFIYSK
  [4]: NYKDTAPVLDSDGSY
  [5]: NYKDTAPVLDSDGSY
  [6]: SDGSYFIYSKLNMKTSKWE
  [7]: SDGSYFIYSKLNMKTSKWE
  [8]: DSDGSYFIYSK
  [9]: DSDGSYFIYSK
  [10]: SDGSYFIYSK
  [11]: SDGSYFIYSK
  [12]: NMKTSKWEKTDS
  [13]: NMKTSKWEKTDS
  [14]: NMKTSKWEKTDS
  [15]: NMKTSKWEKTDS
  [16]: NMKTSKWEKTDS
  [17]: EWTSNGHTEENYKDTAPVL
  [18]: YKDTAPVLDSDGSY
  [19]: WTSNGHTEENYKDTAPVL
  [20]: WTSNGHTEENYKDTAPVL
  [21]: KDTAPVLDSDGSYFIYS
  [22]: DTAPVLDSDGSYF
  [23]: NYKDTAPVLD
  [24]: NYKDTAPVLD
  [25]: KDTAPVLDSDGSYFIYSKLNM
  [26]: FIYSKLNMKTSKWEKTDS
  [27]: FIYSKLNMKTSKWEKTDS
  [28]: NYKDTAPVLDSD
  [29]: KTSKWEKTDS
  [30]: KTSKWEKTDS
  [31]: KTSKWEKTDS
  [32]: KTSKWEKTDS
  [33]: VEWTSNGHTEENYKDTAPVL
  [34]: TDSFSCNV
  [35]: TDSFSCNV
  [36]: ENYKDTAPVLD
  [37]: NYKDTAPVL
  [38]: NYKDTAPVL
  [39]: YKDTAPVL
  [40]: YKDTAPVL
  [41]: VVGFNPGDIS
  [42]: FIYSKLNM
  [43]: FIYSKLNM
  [44]: FNPGDISVE
  [45]: NMKTSKW
  [46]: IYSKLNM
  [47]: SDGSYFIYSKLN
  Peptides: FNPGDISVE,VVGFNPGDIS,VEWTSNGHTEENYKDTAPVL,YKDTAPVL,KTSKWEKTDS,EWTSNGHTEENYKDTAPVL,VVGFNPGDISV,IYSKLNM,NMKTSKWEKTDS,NYKDTAPVLD,DSDGSYFIYSK,SDGSYFIYSK,DTAPVLDSDGSYFIYSK,ENYKDTAPVLD,NMKTSKW,VVGFNPGDISVE,NYKDTAPVL,SDGSYFIYSKLNMKTSKWE,FIYSKLNMKTSKWEKTDS,KDTAPVLDSDGSYFIYSKLNM,WTSNGHTEENYKDTAPVL,FIYSKLNM,NYKDTAPVLDSD,YKDTAPVLDSDGSY,TDSFSCNV,DTAPVLDSDGSYF,KDTAPVLDSDGSYFIYS,SDGSYFIYSKLN,NYKDTAPVLDSDGSY
  Total Peptides: 29
# Seed[3][5]: HEGLKNYYLKKTISRSPG -> E[154.183]HEGIENYYIKKTISRSPG
  [0]: YYLKKTISRSPG
  [1]: LKKTISRSPG
  [2]: YLKKTISRSPG
  [3]: YLKKTISRSPG
  [4]: KKTISRSPG
  [5]: HEGLKNYYLK
  [6]: GLKNYYLK
  Peptides: YLKKTISRSPG,LKKTISRSPG,GLKNYYLK,HEGLKNYYLK,YYLKKTISRSPG,KKTISRSPG
  Total Peptides: 6
# Num Classes: 4
# Unique Peptides: 744
# Final Seq: [312.075]IQKSGAEIMKPGASVKISCKATGYTFTGYWIEWVKQRPGHGIEWIGEISPGSGSTNYNEEFQ-[316.128]IWNEQFKGKATFTADTSSNQAYIQISSIT[216.095]-[200.091]SSAQTTP[184.07]VYPIAPGCGDTTGSSVTIGCIVKGYFPESVTVTWNSGSISSSVHTFPAIIQSGIYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPSGPISTINPCPPCKECHKCPAPNIEGGPSVFIFPPNIKDVIMISITPKVTC-VVDVSEDDPDVQ[351.139]-FVNNVEVHTAQTQTHRE-RVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSL-VVGFNPGDISVEWTSNGHTEENYKDTAPVIDSDGSYFIYSKINMKTSKWEKTDSFSCNVV-E[154.183]HEGIENYYIKKTISRSPG
# Sitewise Support: -2 4 6 8 11 12 12 12 13 13 13 10 7 8 8 10 7 4 4 3 3 4 4 4 4 4 4 2 2 4 14 20 20 26 29 29 26 26 26 26 29 29 28 26 20 14 14 11 10 10 9 5 5 5 5 5 7 7 5 5 5 5 3 -2 3 5 6 7 6 5 4 2 2 2 2 3 2 3 5 7 5 1 1 4 8 8 8 6 6 3 3 4 4 1 -5 5 1 4 15 24 24 25 25 25 23 21 18 18 18 18 17 16 17 19 18 18 19 21 19 19 20 22 22 26 34 35 24 24 27 27 27 41 43 47 74 80 83 97 112 114 122 123 126 132 130 130 129 125 118 101 101 101 78 56 32 32 29 28 17 15 15 12 13 16 16 15 15 15 15 15 15 15 13 13 10 8 7 11 20 22 22 24 24 25 25 25 26 25 24 25 28 69 84 84 86 88 90 90 90 93 94 88 89 84 84 86 86 86 77 51 32 28 25 26 26 26 26 25 25 24 28 28 28 29 29 30 37 37 38 38 38 38 32 28 21 21 18 18 18 18 18 18 18 4 4 3 -1 1 1 2 2 1 1 2 3 3 2 2 1 -2 4 4 4 4 4 9 9 7 5 5 5 5 5 5 5 5 -1 22 26 29 31 37 43 43 43 43 43 43 41 30 26 25 21 15 6 5 3 6 15 15 18 21 26 26 27 27 27 28 28 26 14 16 16 10 7 7 8 11 11 11 20 20 20 20 22 22 22 22 22 22 22 22 22 19 13 11 1 1 1 1 1 -4 4 4 5 5 5 5 5 5 5 5 4 4 4 4 4 4 4 4 4 5 12 15 17 19 19 19 19 19 19 13 15 15 14 14 14 15 15 15 15 14 9 15 14 14 14 14 14 14 14 12 15 15 16 5 5 2 2 2 0 -3 3 3 3 3 3 5 5 6 8 6 7 5 5 5 5 5 5 5 5 
# Sitewise Overlap: -2 6 6 8 11 12 12 12 13 13 13 10 7 8 8 10 7 4 4 3 3 4 4 4 4 4 4 2 2 4 14 20 20 26 29 29 26 26 31 31 31 31 29 26 22 16 16 13 10 10 10 10 10 10 8 8 8 8 8 8 7 7 5 -5 6 6 7 7 7 7 6 6 6 5 4 4 3 5 7 7 7 11 11 10 10 10 8 8 8 5 5 5 5 5 -6 7 7 9 15 25 25 25 25 25 23 21 18 18 18 18 17 16 17 19 18 18 19 21 19 19 20 22 22 26 34 35 24 24 27 27 27 41 43 47 74 80 83 97 112 114 122 123 126 132 130 130 129 125 118 101 101 101 78 56 32 32 29 28 17 15 15 12 13 16 16 15 15 15 15 15 15 15 13 13 10 8 7 11 20 22 22 24 24 25 25 25 26 25 24 25 28 69 84 84 86 88 90 90 90 93 94 88 89 84 84 86 86 86 77 51 32 28 25 26 26 26 26 25 25 24 28 28 28 29 29 30 37 37 38 38 38 38 32 28 21 21 18 18 18 18 18 18 18 4 4 3 -1 1 1 2 2 4 4 4 4 4 4 4 3 -2 4 4 4 4 4 9 9 7 5 5 5 5 5 5 5 5 -1 22 26 29 31 37 43 43 43 43 43 43 41 30 26 25 21 15 6 5 3 6 15 15 18 21 26 26 27 27 27 28 28 26 14 16 16 10 7 7 8 11 11 11 20 20 20 20 22 22 22 22 22 22 22 22 22 19 13 11 1 1 1 1 1 -4 4 4 5 5 5 5 5 5 5 5 4 4 4 4 4 4 4 4 4 5 12 15 17 19 19 19 19 19 19 13 15 15 14 14 14 15 15 15 15 14 9 15 14 14 14 14 14 14 14 12 16 16 16 5 5 5 5 5 3 -3 3 4 4 5 5 5 5 6 8 6 7 5 5 5 5 5 5 5 5 
# FinalLen: 421
# % Correct: 0.25653206650831356

### Path 1 ###
# Templates 0:1.Mouse_Rat_LC.AJ235948|IGKV8-30*01|Mus musculus_C3H|F|V-REGION|441..745|305 nt| seeds: 
# Template: DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSYP
# Seed[0][0]: DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSY -> DIVMSQSPSSIAVSVGEKVTMSCKSSQSIIYSSNQKNYIAWYQQKPGQSPKIIIYWASTRESGVPDRFTGSGSGTDFTITISSVKAEDIAVYYCQQYYSY[253.143]
  [0]: DIVMSQSPSSLAVSVGEK
  [1]: DIVMSQSPSSLAVSVGEK
  [2]: DIVMSQSPSSLAVSVGEK
  [3]: DIVMSQSPSSLAVSVGEK
  [4]: DIVMSQSPSSLAVSVGEK
  [5]: DIVMSQSPSSLAVSVGEK
  [6]: DIVMSQSPSSLAVSVGEK
  [7]: DIVMSQSPSSLAVSVGEK
  [8]: DIVMSQSPSSLAVSVGEK
  [9]: DIVMSQSPSSLAVSVGEK
  [10]: DIVMSQSPSSLAVSVGEK
  [11]: DIVMSQSPSSLAVSVGEK
  [12]: DIVMSQSPSSLAVSVGEK
  [13]: DIVMSQSPSSLAVSVGEK
  [14]: DIVMSQSPSSLAVSVGEK
  [15]: DIVMSQSPSSLAVSVGEK
  [16]: DIVMSQSPSSLAVSVGEK
  [17]: DIVMSQSPSSLAVSVGEK
  [18]: DIVMSQSPSSLAVSVGEK
  [19]: DIVMSQSPSSLAVSVGEK
  [20]: DIVMSQSPSSLAVSVGEK
  [21]: DIVMSQSPSSLAVSVGEK
  [22]: DIVMSQSPSSLAVSVGEK
  [23]: DIVMSQSPSSLAVSVGEK
  [24]: DIVMSQSPSSLAVSVGEK
  [25]: DIVMSQSPSSLAVSVGEK
  [26]: DIVMSQSPSSLAVSVGEK
  [27]: DIVMSQSPSSLAVSVGEK
  [28]: DIVMSQSPSSLAVSVGEK
  [29]: DIVMSQSPSSLAVSVGEK
  [30]: DIVMSQSPSSLAVSVGEK
  [31]: SQSPSSLAVSVGEK
  [32]: SQSPSSLAVSVGEK
  [33]: SQSPSSLAVSVGEK
  [34]: SQSPSSLAVSVGEK
  [35]: SQSPSSLAVSVGEK
  [36]: SQSPSSLAVSVGEK
  [37]: SQSPSSLAVSVGEK
  [38]: SQSPSSLAVSVGEK
  [39]: SQSPSSLAVSVGEK
  [40]: IVMSQSPSSLAVSVGEK
  [41]: QSPSSLAVSVGEK
  [42]: QSPSSLAVSVGEK
  [43]: QSPSSLAVSVGEK
  [44]: SQSPSSLAVSVGEKVTMSC
  [45]: DIVMSQSPSSLAVSVGE
  [46]: DIVMSQSPSSLAVSVGE
  [47]: DIVMSQSPSSLAVSVGE
  [48]: DIVMSQSPSSLAVSVGE
  [49]: DIVMSQSPSSLAVSVGE
  [50]: DIVMSQSPSSLAVSVGE
  [51]: DIVMSQSPSSLAVSVGE
  [52]: DIVMSQSPSSLAVSVGE
  [53]: DIVMSQSPSSLAVSVGE
  [54]: DIVMSQSPSSLAVSVGE
  [55]: DIVMSQSPSSLAVSVGE
  [56]: DIVMSQSPSSLAVSVGE
  [57]: DIVMSQSPSSLAVSVGE
  [58]: DIVMSQSPSSLAVSVGE
  [59]: DIVMSQSPSSLAVSVGE
  [60]: DIVMSQSPSSLAVSVGE
  [61]: DIVMSQSPSSLAVSVGE
  [62]: DIVMSQSPSSLAVSVGE
  [63]: DIVMSQSPSSLAVSVGEKVTM
  [64]: DIVMSQSPSSLAVSVGEKVTM
  [65]: DIVMSQSPSSLAVSVGEKVTM
  [66]: SPSSLAVSVGEK
  [67]: SPSSLAVSVGEK
  [68]: SPSSLAVSVGEK
  [69]: DIVMSQSPSSLAVSVGEKVTMSC
  [70]: DIVMSQSPSSLAVSVGEKVTMSC
  [71]: DIVMSQSPSSLAVSVGEKVT
  [72]: DIVMSQSPSSLAVSVGEKVT
  [73]: AVSVGEKVTM
  [74]: AVSVGEKVTM
  [75]: AVSVGEKVTM
  [76]: AVSVGEKVTM
  [77]: AVSVGEKVTM
  [78]: AVSVGEKVTM
  [79]: AVSVGEKVTM
  [80]: AVSVGEKVTM
  [81]: AVSVGEKVTM
  [82]: AVSVGEKVTM
  [83]: AVSVGEKVTM
  [84]: SQSPSSLAVSVGEKVTM
  [85]: KVTMSCKSSQSLL
  [86]: YQQKPGQSPKLLIYW
  [87]: LAWYQQKPGQSPK
  [88]: LAWYQQKPGQSPK
  [89]: LAWYQQKPGQSPK
  [90]: AWYQQKPGQSPK
  [91]: AWYQQKPGQSPK
  [92]: SSQSLLYSSNQKNYLAWYQQKPGQSPK
  [93]: SSQSLLYSSNQKNYLAWYQQKPGQSPK
  [94]: PGQSPKLLIYWASTR
  [95]: PGQSPKLLIYWASTR
  [96]: PGQSPKLLIYWASTR
  [97]: PGQSPKLLIYWASTR
  [98]: LAVSVGEKVTM
  [99]: LAVSVGEKVTM
  [100]: LAVSVGEKVTM
  [101]: LLIYWASTR
  [102]: LLIYWASTR
  [103]: LLIYWASTR
  [104]: LLIYWASTR
  [105]: LLIYWASTR
  [106]: LLIYWASTR
  [107]: LLIYWASTR
  [108]: LLIYWASTR
  [109]: LLIYWASTR
  [110]: LLIYWASTR
  [111]: LLIYWASTR
  [112]: LLIYWASTR
  [113]: LLIYWASTR
  [114]: LLIYWASTR
  [115]: LLIYWASTR
  [116]: LLIYWASTR
  [117]: LLIYWASTR
  [118]: LLIYWASTR
  [119]: LLIYWASTR
  [120]: LLIYWASTR
  [121]: LLIYWASTR
  [122]: LLIYWASTR
  [123]: LLIYWASTR
  [124]: LLIYWASTR
  [125]: LLIYWASTR
  [126]: LLIYWASTR
  [127]: LLIYWASTR
  [128]: LLIYWASTR
  [129]: LLIYWASTR
  [130]: LLIYWASTR
  [131]: LLIYWASTR
  [132]: LLIYWASTR
  [133]: IVMSQSPSSL
  [134]: DIVMSQSPSSL
  [135]: DIVMSQSPSSL
  [136]: DIVMSQSPSSL
  [137]: DIVMSQSPSSL
  [138]: DIVMSQSPSSL
  [139]: DIVMSQSPSSL
  [140]: DIVMSQSPSSLA
  [141]: DIVMSQSPSSLA
  [142]: DIVMSQSPSSLA
  [143]: DIVMSQSPSSLA
  [144]: DIVMSQSPSSLA
  [145]: DIVMSQSPSSLA
  [146]: SCKSSQSLLY
  [147]: SCKSSQSLLY
  [148]: VSVGEKVTM
  [149]: VSVGEKVTM
  [150]: VSVGEKVTM
  [151]: DIVMSQSPSSLAV
  [152]: SLAVSVGEK
  [153]: RESGVPDRFTGSGSGTDFTLTISSVK
  [154]: FTGSGSGTDFTLTISSVK
  [155]: FTGSGSGTDFTLTISSVK
  [156]: FTGSGSGTDFTLTISSVK
  [157]: FTGSGSGTDFTLTISSVK
  [158]: FTGSGSGTDFTLTISSVK
  [159]: FTGSGSGTDFTLTISSVK
  [160]: FTGSGSGTDFTLTISSVK
  [161]: FTGSGSGTDFTLTISSVK
  [162]: FTGSGSGTDFTLTISSVK
  [163]: FTGSGSGTDFTLTISSVK
  [164]: FTGSGSGTDFTLTISSVK
  [165]: FTGSGSGTDFTLTISSVK
  [166]: FTGSGSGTDFTLTISSVK
  [167]: FTGSGSGTDFTLTISSVK
  [168]: FTGSGSGTDFTLTISSVK
  [169]: FTGSGSGTDFTLTISSVK
  [170]: FTGSGSGTDFTLTISSVK
  [171]: FTGSGSGTDFTLTISSVK
  [172]: FTGSGSGTDFTLTISSVK
  [173]: FTGSGSGTDFTLTISSVK
  [174]: SGVPDRFTGSGSGTDF
  [175]: GSGSGTDFTLTISSVKAE
  [176]: TLTISSVKAEDL
  [177]: FTLTISSVKAED
  [178]: FTLTISSVKAE
  [179]: TLTISSVKAED
  [180]: LTISSVKAEDL
  [181]: SGVPDRFTGSGSGTDFTLTISSVKAE
  [182]: KLLIYWASTR
  [183]: SCKSSQSLL
  [184]: SCKSSQSLL
  [185]: SCKSSQSLL
  [186]: SCKSSQSLL
  [187]: FTLTISSVKAEDL
  [188]: TISSVKAEDL
  [189]: SQSPSSLAVSVGE
  [190]: KLLIYWAST
  [191]: AEDLAVYYCQQY
  [192]: DIVMSQSPSS
  [193]: IYWASTR
  [194]: IYWASTR
  [195]: IYWASTR
  [196]: IYWASTR
  [197]: IYWASTR
  [198]: LIYWASTR
  [199]: LIYWASTR
  [200]: DIVMSQSPS
  [201]: MSCKSSQSLLY
  [202]: SCKSSQSL
  [203]: YCQQYYSY
  [204]: KSSQSLLY
  [205]: YQQKPGQSPKLL
  [206]: YQQKPGQSPKLL
  [207]: IVMSQSPSSLAVSVGE
  [208]: LAVSVGEKVT
  [209]: DIVMSQSPSSLAVSVGEKVV->H
  [210]: FTGSGSGTDFTLT
  [211]: YQQKPGQSPK
  [212]: TISSVKAEDLAV
  [213]: TLTISSVKAEDLAVY
  [214]: QKNN->YYLAWYQQKPGQSPKLLIYWASTR
  [215]: SSQSLLYSSNQQ->VKNYLAWYQQKPGQSPK
  [216]: KSSQSLLYSSNN->A
  [217]: YQQKPGQSPKLL
  [218]: LAWYQQKPGQSPKLL
  [219]: SSQSLLYSS->GSNQK
  [220]: DIVMSQSPSSLAVSVGEK
  [221]: DIVMSQSPSSLAVSVGEK
  [222]: DIVMSQSPSSLAVSVGEKVV->H
  [223]: QKNN->RYLAWYQQKPGQSPKLLIYWASTR
  [224]: QKNN->YYLAWYQQKPGQSPKLLIYWASTR
  [225]: YQQKPGQSPKLL
  [226]: NYLAWYQQ->WQKPGQSPKLLIYWASTR
  [227]: SCKSSQSLL
  [228]: TLTISSVKAEDLAV
  [229]: SSQSLLYSSNQKNYLAWYQQKPGQSPK
  [230]: FTLTISSVKAEDL
  [231]: DIVMSQSPSSLAVSVGEK
  [232]: KPGQSPKK->YLLIYWASTR
  [233]: AVSVGEKVTM
  [234]: AWYQQKPGQSPKL
  [235]: SCKSSQSL
  [236]: AVSVGEKVTM
  [237]: IYWASTR
  [238]: SSQSLLYSS->GSNQK
  [239]: IYWASTR
  [240]: FTGSGSGTDFTLTISSVK
  [241]: FTLTISSVKAEDL
  [242]: DIVMSQSPSSLAVSVGEK
  [243]: QSPSSLAVSVGE
  [244]: AWYQQKPGQSPK
  [245]: DIVMSQSPS
  [246]: NYLAWYQQKPGQSPK
  [247]: YQQKPGQSPKLLI
  [248]: DIVMSQSPS
  [249]: AVSVGEKVTM
  [250]: KSSQSLLYSSNQQ->P
  Peptides: VSVGEKVTM,NYLAWYQQKPGQSPKLLIYWASTR,TLTISSVKAEDL,FTLTISSVKAEDL,SLAVSVGEK,FTGSGSGTDFTLTISSVK,FTGSGSGTDFTLT,KPGQSPKLLIYWASTR,NYLAWYQQKPGQSPK,KLLIYWAST,AEDLAVYYCQQY,DIVMSQSPS,LAVSVGEKVT,GSGSGTDFTLTISSVKAE,QSPSSLAVSVGE,FTLTISSVKAE,TLTISSVKAED,SQSPSSLAVSVGEK,SCKSSQSLLY,DIVMSQSPSSLAVSVGEKVTMSC,DIVMSQSPSSLAVSVGEK,DIVMSQSPSSLAVSVGEKVTM,KLLIYWASTR,LAWYQQKPGQSPKLL,AWYQQKPGQSPKL,KSSQSLLYSSNQ,SPSSLAVSVGEK,DIVMSQSPSSLAVSVGEKVT,SQSPSSLAVSVGEKVTM,YQQKPGQSPKLLIYW,KVTMSCKSSQSLL,AVSVGEKVTM,SQSPSSLAVSVGE,LAVSVGEKVTM,TLTISSVKAEDLAVY,IYWASTR,PGQSPKLLIYWASTR,YCQQYYSY,TLTISSVKAEDLAV,IVMSQSPSSLAVSVGE,LLIYWASTR,DIVMSQSPSSL,SCKSSQSL,QKNYLAWYQQKPGQSPKLLIYWASTR,AWYQQKPGQSPK,MSCKSSQSLLY,SGVPDRFTGSGSGTDFTLTISSVKAE,SSQSLLYSSNQKNYLAWYQQKPGQSPK,DIVMSQSPSSLA,IVMSQSPSSL,YQQKPGQSPK,SSQSLLYSSNQK,IVMSQSPSSLAVSVGEK,DIVMSQSPSSLAV,SQSPSSLAVSVGEKVTMSC,QSPSSLAVSVGEK,YQQKPGQSPKLLI,KSSQSLLYSSN,KSSQSLLY,RESGVPDRFTGSGSGTDFTLTISSVK,DIVMSQSPSSLAVSVGE,FTLTISSVKAED,SCKSSQSLL,SGVPDRFTGSGSGTDF,LTISSVKAEDL,YQQKPGQSPKLL,LIYWASTR,DIVMSQSPSSLAVSVGEKV,DIVMSQSPSS,TISSVKAEDLAV,TISSVKAEDL,LAWYQQKPGQSPK
  Total Peptides: 72
# Templates 1:2.Mouse_Rat_LC.V00777|IGKJ1*01|Mus musculus|F|J-REGION|740..777|38 nt|2| | | |12 seeds: 
# Template: WTFGGGTKLEIK
# Seed[1][0]: TFGGGTKLEIK -> [273.767]YSYPRTFGGGTQIEIKR
  [0]: TFGGGTKLEIK
  [1]: TFGGGTKLEIK
  [2]: TFGGGTKLEIK
  [3]: TFGGGTKLEIK
  [4]: TFGGGTKLEIK
  [5]: TFGGGTKLEIK
  [6]: TFGGGTKLEIK
  [7]: FGGGTKLEIK
  [8]: FGGGTKLEIK
  [9]: GGGTKLEIK
  [10]: GGGTKLEIK
  Peptides: GGGTKLEIK,FGGGTKLEIK,TFGGGTKLEIK
  Total Peptides: 3
# Templates 2:3.Mouse_Rat_LC.V00807|IGKC*01|Mus musculus|F|C-REGION|211..530|320 nt|1|+1|0| |1 seeds: 
# Template: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
# Seed[2][0]: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC -> RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
  [0]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [1]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [2]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [3]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [4]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [5]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [6]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [7]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [8]: SGGASVVCFLNNFYPKD
  [9]: SGGASVVCFLNNFYPKD
  [10]: SGGASVVCFLNNFYPKD
  [11]: SGGASVVCFLNNFYPKD
  [12]: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPK
  [13]: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPK
  [14]: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPK
  [15]: RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPK
  [16]: SGGASVVCFLNNFYPK
  [17]: SGGASVVCFLNNFYPK
  [18]: SGGASVVCFLNNFYPK
  [19]: SGGASVVCFLNNFYPK
  [20]: SGGASVVCFLNNFYPK
  [21]: SGGASVVCFLNNFYPK
  [22]: SGGASVVCFLNNFYPK
  [23]: SGGASVVCFLNNFYPK
  [24]: SGGASVVCFLNNFYPK
  [25]: SGGASVVCFLNNFYPK
  [26]: DINVKWKIDGSER
  [27]: DINVKWKIDGSER
  [28]: DINVKWKIDGSER
  [29]: QLTSGGASVVCFLNNFYPKD
  [30]: QLTSGGASVVCFLNNFYPKD
  [31]: SGGASVVCFLNNFYPKDINVK
  [32]: RQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE
  [33]: DSTYSMSSTLTLTKDEYER
  [34]: DSTYSMSSTLTLTKDEYER
  [35]: DSTYSMSSTLTLTKDEYER
  [36]: DSTYSMSSTLTLTKDEYER
  [37]: DSTYSMSSTLTLTKDEYER
  [38]: DSTYSMSSTLTLTKDEYER
  [39]: DSTYSMSSTLTLTKDEYER
  [40]: DSTYSMSSTLTLTKDEYER
  [41]: DSTYSMSSTLTLTKDEYER
  [42]: DSTYSMSSTLTLTKDEYER
  [43]: DSTYSMSSTLTLTKDEYER
  [44]: DSTYSMSSTLTLTKDEYER
  [45]: DSTYSMSSTLTLTKDEYER
  [46]: DSTYSMSSTLTLTKDEYER
  [47]: DSTYSMSSTLTLTKDEYER
  [48]: DSTYSMSSTLTLTKDEYER
  [49]: DSTYSMSSTLTLTKDEYER
  [50]: DSTYSMSSTLTLTKDEYER
  [51]: DSTYSMSSTLTLTKDEYER
  [52]: SKDSTYSMSSTLTLTKDE
  [53]: SKDSTYSMSSTLTLTKDE
  [54]: NSWTDQDSKDSTYSM
  [55]: SMSSTLTLTKDEYER
  [56]: SMSSTLTLTKDEYER
  [57]: SMSSTLTLTKDEYER
  [58]: SMSSTLTLTKDEYER
  [59]: SMSSTLTLTKDEYER
  [60]: QNGVLNSWTDQDSK
  [61]: QNGVLNSWTDQDSK
  [62]: QNGVLNSWTDQDSK
  [63]: QNGVLNSWTDQDSK
  [64]: QNGVLNSWTDQDSK
  [65]: QNGVLNSWTDQDSK
  [66]: DSTYSMSSTLTLTK
  [67]: DSTYSMSSTLTLTK
  [68]: DSTYSMSSTLTLTK
  [69]: DSTYSMSSTLTLTK
  [70]: DSTYSMSSTLTLTK
  [71]: DSTYSMSSTLTLTK
  [72]: DSTYSMSSTLTLTK
  [73]: DSTYSMSSTLTLTK
  [74]: DSTYSMSSTLTLTK
  [75]: DSTYSMSSTLTLTK
  [76]: DSTYSMSSTLTLTK
  [77]: DSTYSMSSTLTLTK
  [78]: DSTYSMSSTLTLTK
  [79]: DSTYSMSSTLTLTK
  [80]: DSTYSMSSTLTLTK
  [81]: DSTYSMSSTLTLTK
  [82]: DSTYSMSSTLTLTK
  [83]: DSTYSMSSTLTLTK
  [84]: DSTYSMSSTLTLTK
  [85]: DSTYSMSSTLTLTK
  [86]: GVLNSWTDQDSKDSTYS
  [87]: NSWTDQDSKDSTYSMSSTL
  [88]: NSWTDQDSKDSTYSMSSTL
  [89]: NSWTDQDSKDSTYSMSSTL
  [90]: NSWTDQDSKDSTYSMSSTL
  [91]: NSWTDQDSKDSTYSMSSTL
  [92]: NGVLNSWTDQDSKDSTYS
  [93]: NSWTDQDSKDSTYSMSST
  [94]: NSWTDQDSKDSTYSMSST
  [95]: NSWTDQDSKDSTYSMSST
  [96]: GVLNSWTDQDSKDSTY
  [97]: GVLNSWTDQDSKDSTY
  [98]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [99]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [100]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [101]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [102]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [103]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [104]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [105]: QNGVLNSWTDQDSKDSTYSMSSTLTLTK
  [106]: TYSMSSTLTLTKDEYER
  [107]: TYSMSSTLTLTKDEYER
  [108]: NSWTDQDSKDSTY
  [109]: NSWTDQDSKDSTY
  [110]: NGVLNSWTDQDSKD
  [111]: NGVLNSWTDQDSKD
  [112]: NGVLNSWTDQDSKD
  [113]: NSWTDQDSKDSTYSMS
  [114]: NSWTDQDSKDSTYSMS
  [115]: QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYER
  [116]: QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYER
  [117]: QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYER
  [118]: WTDQDSKDSTYSMSSTL
  [119]: WTDQDSKDSTYSMSSTL
  [120]: SSTLTLTKDEYER
  [121]: SSTLTLTKDEYER
  [122]: SSTLTLTKDEYER
  [123]: NSWTDQDSKDST
  [124]: NSWTDQDSKDST
  [125]: VLNSWTDQDSKD
  [126]: STYSMSSTLTLTKDE
  [127]: STYSMSSTLTLTKDE
  [128]: STYSMSSTLTLTKDE
  [129]: STYSMSSTLTLTKDE
  [130]: STYSMSSTLTLTKDE
  [131]: STYSMSSTLTLTKDE
  [132]: STYSMSSTLTLTKDE
  [133]: STYSMSSTLTLTKDE
  [134]: STYSMSSTLTLTKDE
  [135]: STYSMSSTLTLTKDE
  [136]: STYSMSSTLTLTKDE
  [137]: STYSMSSTLTLTKDE
  [138]: STYSMSSTLTLTKDE
  [139]: STYSMSSTLTLTKDE
  [140]: STYSMSSTLTLTKDE
  [141]: STYSMSSTLTLTKDE
  [142]: STYSMSSTLTLTKDE
  [143]: STYSMSSTLTLTKDE
  [144]: STYSMSSTLTLTKDE
  [145]: STYSMSSTLTLTKDE
  [146]: STYSMSSTLTLTKDE
  [147]: STYSMSSTLTLTKDE
  [148]: STYSMSSTLTLTKDE
  [149]: STYSMSSTLTLTKDE
  [150]: STYSMSSTLTLTKDE
  [151]: STYSMSSTLTLTKDE
  [152]: STYSMSSTLTLTKDE
  [153]: STYSMSSTLTLTKDE
  [154]: STYSMSSTLTLTKDE
  [155]: NFYPKDINVKWKID
  [156]: NFYPKDINVKWKID
  [157]: GVLNSWTDQDSKD
  [158]: GVLNSWTDQDSKD
  [159]: GVLNSWTDQDSKD
  [160]: WTDQDSKDSTYSM
  [161]: WTDQDSKDSTYSM
  [162]: GVLNSWTDQDSK
  [163]: GVLNSWTDQDSK
  [164]: GVLNSWTDQDSK
  [165]: RQNGVLNSWTDQDSKD
  [166]: RQNGVLNSWTDQDSKD
  [167]: RQNGVLNSWTDQDSKD
  [168]: RQNGVLNSWTDQDSKD
  [169]: RQNGVLNSWTDQDSKD
  [170]: RQNGVLNSWTDQDSKD
  [171]: IDGSERQNGVLNSWTDQDSK
  [172]: IDGSERQNGVLNSWTDQDSK
  [173]: IDGSERQNGVLNSWTDQDSK
  [174]: IDGSERQNGVLNSWTDQDSK
  [175]: IDGSERQNGVLNSWTDQDSK
  [176]: IDGSERQNGVLNSWTDQDSK
  [177]: GASVVCFLNNFYPK
  [178]: GASVVCFLNNFYPK
  [179]: GASVVCFLNNFYPK
  [180]: GASVVCFLNNFYPK
  [181]: GASVVCFLNNFYPK
  [182]: VLNSWTDQDSK
  [183]: NGVLNSWTDQDSK
  [184]: NGVLNSWTDQDSK
  [185]: NGVLNSWTDQDSK
  [186]: DSKDSTYSMSSTL
  [187]: DSKDSTYSMSSTL
  [188]: STLTLTKDEYER
  [189]: STLTLTKDEYER
  [190]: STLTLTKDEYER
  [191]: STLTLTKDEYER
  [192]: RADAAPTVSIFPPSSEQLT
  [193]: QNGVLNSWTDQDSKD
  [194]: LNNFYPKDINVKW
  [195]: LNNFYPKDINVKW
  [196]: LNNFYPKDINVKW
  [197]: LNNFYPKDINVKW
  [198]: LNNFYPKDINVKW
  [199]: LNNFYPKDINVKW
  [200]: LNNFYPKDINVKW
  [201]: LNNFYPKDINVKW
  [202]: LNNFYPKDINVKW
  [203]: WKIDGSERQNGVLNSWTDQDSK
  [204]: WKIDGSERQNGVLNSWTDQDSK
  [205]: WKIDGSERQNGVLNSWTDQDSK
  [206]: MSSTLTLTKDEYE
  [207]: IFPPSSEQLTSGGASVVCF
  [208]: IFPPSSEQLTSGGASVVCF
  [209]: IFPPSSEQLTSGGASVVCF
  [210]: IFPPSSEQLTSGGASVVCF
  [211]: TDQDSKDSTY
  [212]: TDQDSKDSTY
  [213]: TDQDSKDSTY
  [214]: TDQDSKDSTY
  [215]: TDQDSKDSTY
  [216]: GVLNSWTDQDSKDSTYSMS
  [217]: DSTYSMSSTLT
  [218]: DSTYSMSSTLT
  [219]: DSTYSMSSTLT
  [220]: SKDSTYSMSSTLT
  [221]: NNFYPKDINVKW
  [222]: NNFYPKDINVKW
  [223]: TSGGASVVCFLNNFYPK
  [224]: DSKDSTYSMSSTLT
  [225]: DSKDSTYSMSSTLT
  [226]: STLTLTKDEYE
  [227]: STLTLTKDEYE
  [228]: MSSTLTLTKDEYER
  [229]: MSSTLTLTKDEYER
  [230]: SWTDQDSKDSTYSMS
  [231]: STYSMSSTLT
  [232]: STYSMSSTLTLTKDEYE
  [233]: QNGVLNSWTDQDSKDSTYSMS
  [234]: YPKDINVKWKIDGSE
  [235]: YPKDINVKWKIDGSE
  [236]: YPKDINVKWKIDGSE
  [237]: SKDSTYSMSST
  [238]: INVKWKIDGSE
  [239]: INVKWKIDGSE
  [240]: INVKWKIDGSE
  [241]: LNNFYPKDINVKWKIDGSE
  [242]: LNNFYPKDINVKWKIDGSE
  [243]: LNNFYPKDINVKWKIDGSE
  [244]: LNNFYPKDINV
  [245]: LNNFYPKDINV
  [246]: SMSSTLTLTK
  [247]: SMSSTLTLTK
  [248]: IFPPSSEQLTSGGAS
  [249]: IFPPSSEQLTSGGAS
  [250]: NSWTDQDSKDSTYSMSSTLT
  [251]: SMSSTLTLTKDEYE
  [252]: LNNFYPKDINVK
  [253]: LNNFYPKDINVK
  [254]: LNNFYPKDINVK
  [255]: NFYPKDINVKWK
  [256]: NFYPKDINVKWK
  [257]: NSWTDQDSKD
  [258]: NSWTDQDSKD
  [259]: AAPTVSIFPPSSE
  [260]: SKDSTYSMSSTL
  [261]: SKDSTYSMSSTL
  [262]: NGVLNSWTDQD
  [263]: NGVLNSWTDQD
  [264]: NNFYPKDINVKWKID
  [265]: NFYPKDINVKWKIDGSE
  [266]: NFYPKDINVKWKIDGSE
  [267]: NSWTDQDSK
  [268]: DQDSKDSTYSMSSTLT
  [269]: NFYPKDINVKW
  [270]: WKIDGSER
  [271]: WKIDGSER
  [272]: WKIDGSER
  [273]: WKIDGSER
  [274]: NNFYPKDINVK
  [275]: SGGASVVCFLNNFYPKDINVKWKID
  [276]: GVLNSWTDQD
  [277]: GVLNSWTDQD
  [278]: VKWKIDGSE
  [279]: VKWKIDGSE
  [280]: RQNGVLNSWTDQD
  [281]: RQNGVLNSWTDQD
  [282]: RQNGVLNSWTDQD
  [283]: LNNFYPKDIN
  [284]: LNNFYPKDIN
  [285]: LNNFYPKDIN
  [286]: TYSMSSTLTLTKDE
  [287]: NNFYPKDINVKWKIDGSE
  [288]: NNFYPKDINVKWKIDGSE
  [289]: GVLNSWTDQDSKDSTYSMSSTLTLTKDEYE
  [290]: GSERQNGVLNSWTDQDSKD
  [291]: GSERQNGVLNSWTDQDSKD
  [292]: GSERQNGVLNSWTDQDSKD
  [293]: GSERQNGVLNSWTDQDSKD
  [294]: TLTLTKDEYE
  [295]: TLTLTKDEYE
  [296]: TLTLTKDEYE
  [297]: LNNFYPKDINVKWKID
  [298]: DSKDSTYSMSSTLTLTK
  [299]: FLNNFYPKDIN
  [300]: STLTLTKDE
  [301]: VKWKIDGSERQNGVL
  [302]: VKWKIDGSERQNGVL
  [303]: MSSTLTLTKDE
  [304]: MSSTLTLTKDE
  [305]: TLTKDEYERHN
  [306]: TCEATHKTSTSPIVK
  [307]: TCEATHKTSTSPIVK
  [308]: TCEATHKTSTSPIVK
  [309]: TCEATHKTSTSPIVK
  [310]: TCEATHKTSTSPIVK
  [311]: TCEATHKTSTSPIVKSF
  [312]: TCEATHKTSTSPIVKSF
  [313]: TCEATHKTSTSPIVKSF
  [314]: TCEATHKTSTSPIVKSF
  [315]: TCEATHKTSTSPIVKSF
  [316]: TCEATHKTSTSPIVKSF
  [317]: HNSYTCEATHK
  [318]: HNSYTCEATHK
  [319]: HNSYTCEATHK
  [320]: HNSYTCEATHK
  [321]: HNSYTCEATHK
  [322]: HNSYTCEATHK
  [323]: HNSYTCEATHK
  [324]: HNSYTCEATHK
  [325]: HNSYTCEATHK
  [326]: HNSYTCEATHK
  [327]: HNSYTCEATHK
  [328]: HNSYTCEATHK
  [329]: HNSYTCEATHK
  [330]: HNSYTCEATHK
  [331]: HNSYTCEATHK
  [332]: HNSYTCEATHK
  [333]: HNSYTCEATHK
  [334]: HNSYTCEATHK
  [335]: HNSYTCEATHK
  [336]: HNSYTCEATHK
  [337]: ATHKTSTSPIVKS
  [338]: ATHKTSTSPIVKS
  [339]: ATHKTSTSPIVKSFNRNEC
  [340]: ATHKTSTSPIVKSFNRNEC
  [341]: ATHKTSTSPIVKSFNRNEC
  [342]: ATHKTSTSPIVKSFNRNEC
  [343]: ATHKTSTSPIVKSFNRNEC
  [344]: KTSTSPIVKSF
  [345]: KTSTSPIVKSF
  [346]: KTSTSPIVKSF
  [347]: TSTSPIVKSFNRNEC
  [348]: TSTSPIVKSFNRNEC
  [349]: TSTSPIVKSFNRNEC
  [350]: TSTSPIVKSFNRNEC
  [351]: TSTSPIVKSFNRNEC
  [352]: HNSYTCEATHKTSTSPIVK
  [353]: HNSYTCEATHKTSTSPIVK
  [354]: ATHKTSTSPIVKSFNRNE
  [355]: KTSTSPIVKSFNRNEC
  [356]: KTSTSPIVKSFNRNEC
  [357]: TSTSPIVKSF
  [358]: TSTSPIVKSF
  [359]: SYTCEATHK
  [360]: SYTCEATHK
  [361]: ATHKTSTSPIVK
  [362]: ATHKTSTSPIVK
  [363]: ATHKTSTSPIVK
  [364]: TLTKDEYERHN
  [365]: FLNNFYPK
  [366]: FLNNFYPK
  [367]: FLNNFYPK
  [368]: KSFNRNEC
  [369]: KSFNRNEC
  [370]: KSFNRNEC
  [371]: KSFNRNEC
  [372]: KSFNRNEC
  [373]: KSFNRNEC
  [374]: KSFNRNEC
  [375]: KSFNRNEC
  [376]: KSFNRNEC
  [377]: KSFNRNEC
  [378]: GASVVCFLNNFYPKD
  [379]: SMSSTLTLTKDEYERHNSY
  [380]: SMSSTLTLTKDEYERHNSY
  [381]: LTKDEYER
  [382]: LTKDEYER
  [383]: LTKDEYER
  [384]: LTKDEYER
  [385]: LTKDEYER
  [386]: LTKDEYER
  [387]: LTKDEYER
  [388]: LTKDEYER
  [389]: LTKDEYER
  [390]: SFNRNEC
  [391]: SFNRNEC
  [392]: SFNRNEC
  [393]: SFNRNEC
  [394]: SFNRNEC
  [395]: SFNRNEC
  [396]: KIDGSERQNGVL
  [397]: TSGGASVVCF
  [398]: TSGGASVVCF
  [399]: IFPPSSEQLT
  [400]: IFPPSSEQLT
  [401]: LNNFYPKDINVKWK
  [402]: ATHKTSTSPIV
  [403]: TLTKDEYER
  [404]: TLTKDEYER
  [405]: LNNFYPKD
  [406]: KTSTSPIVKSFN
  [407]: KTSTSPIVKSFN
  [408]: CFLNNFYPKDINVKW
  [409]: SWTDQDSKD
  [410]: GVLNSWTDQDSKDSTYSMSSTLTLTKDE
  [411]: MSSTLTLTK
  [412]: VSIFPPSSEQL
  [413]: VSIFPPSSEQL
  [414]: YPKDINVKWKIDGSERQNGVL
  [415]: NFYPKDINVK
  [416]: NFYPKDINVK
  [417]: SSTLTLTKDE
  [418]: SSTLTLTKDE
  [419]: GSERQNGVLNSWTDQD
  [420]: FLNNFYPKDINVKW
  [421]: LNNFYPK
  [422]: LNNFYPK
  [423]: LNNFYPK
  [424]: LNNFYPK
  [425]: LNNFYPK
  [426]: LNNFYPK
  [427]: LNNFYPK
  [428]: QLTSGGASVVCFL
  [429]: RHNSYTCE
  [430]: RHNSYTCE
  [431]: LNNFYPKDINVKWKIDGSERQNGVL
  [432]: SKDSTYSM
  [433]: INVKWKIDGSERQ
  [434]: FYPKDINVKWKID
  [435]: GSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE
  [436]: IDGSERQNGVLNSWTDQDS
  [437]: TSTSPIVK
  [438]: DAAPTVSIFPPSSEQLT
  [439]: DAAPTVSIFPPSSEQLT
  [440]: DAAPTVSIFPPSSEQLT
  [441]: DINVKWK
  [442]: SYTCEATHKTSTSPIVKSF
  [443]: NGVLNSWTDQDSKDSTY
  [444]: INVKWKID
  [445]: INVKWKID
  [446]: KTSTSPIVK
  [447]: TLTLTKDEYER
  [448]: IFPPSSEQL
  [449]: LNNFYPKDI
  [450]: FLNNFYPKD
  [451]: FLNNFYPKD
  [452]: DINVKWKIDGSERQ
  [453]: IDGSERQNGVLNSWTDQ
  [454]: TSTSPIVKSFN
  [455]: KIDGSERQN
  [456]: WKIDGSE
  [457]: GASVVCFLNNFYPKDINVK
  [458]: KDINVKW
  [459]: KDINVKW
  [460]: KIDGSERQNGVLNSWTDQDSKDSTY
  [461]: YPKDINVKWKIDG
  [462]: NSWTDQDSKDSTYSMSSTLTLTKDEYER
  [463]: TLTKDEYERHNSY
  [464]: IDGSERQNGVLNSWTDQDSKD
  [465]: RQNGVLNS
  [466]: DSTYSMSSTLTLTKDEYER
  [467]: TKDEYERHNSYTCE
  [468]: DSTYSMSSTLTLTK
  [469]: DSTYSMSSTLTLTK
  [470]: STYSMSSTLTLTKDEYER
  [471]: DSTYSMSSTLTLTK
  [472]: TSPIVKSFNRNEC
  [473]: TSTSPIVK
  [474]: TSTSPIVK
  [475]: RQNGVLNSWTDQDSKD
  [476]: SYTCEATHK
  [477]: DSTYSMSSTLTLTK
  [478]: QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYER
  [479]: GGASVVCFLNNFYPK
  [480]: QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYER
  [481]: STSPIVKSF
  [482]: INVKWKIDGSE
  [483]: STYSMSSTLTLTKDE
  [484]: DSTYSMSSTLTLTK
  [485]: TDQDSKDSTY
  [486]: TDQDSKDSTY
  [487]: KTSTSPIVKSFNRNEC
  [488]: ATHKTSTSPIVK
  [489]: ERHNSYTCE
  [490]: ATHKTSTSPIVK
  [491]: SVVCFLNNFYPKDINN->RV
  [492]: TDQDSKDSTY
  [493]: TLTLTKDEYE
  [494]: QNGG->WVLNSWTDQDSKDSTYSMSSTLTLTKDEYER
  [495]: SGGASVVCFLNNFYPKDINVK
  [496]: HNSYTCEATHK
  [497]: DINVKWKIDGSER
  [498]: KTSTSPIVKSFN
  [499]: YPKDINV
  [500]: STYSMSSTLTLTKDE
  [501]: LTLTKDEY
  [502]: TKDEYER
  [503]: STYSMSSTLTLTKDE
  [504]: NGVLNSWTDQDSKDSTY
  [505]: SWTDQDSKDSTYSMSSTLTLTKDE
  [506]: KIDGSERQN
  [507]: TDQDSKDSTY
  [508]: STYSMSSTLTLTKDE
  [509]: AAPTVSIFPPSSE
  [510]: STYSMSSTLTLTKDE
  [511]: STYSMSSTLTLTKDE
  [512]: QNGG->CVLNSWTDQDSK
  [513]: ATHKTSTSPIVK
  [514]: TSPIVKSFNRNEC
  [515]: DSTYSMSSTLTLTK
  [516]: SMSSTLTLTKDEYE
  [517]: KTSTSPIVK
  [518]: STYSMSSTLTLTKDE
  [519]: AAPTVSIFPPSSE
  [520]: WKIDGSER
  [521]: IFPPSSEQLTSGGASVVCFLNNFYPK
  [522]: STYSMSSTLTLTKDE
  [523]: LNNFYPK
  [524]: TSTSPIVK
  [525]: STLTLTKDEYER
  [526]: IDGSERQNGVLNSWTDQDS
  [527]: KTSTSPIVK
  [528]: NFYPKDINVKWK
  [529]: NGVLNSWTDQDS
  [530]: ADAAPTVSIFPPSSEQLT
  [531]: STYSMSSTLTLTKDE
  Peptides: TSPIVKSFNRNEC,GSERQNGVLNSWTDQD,RQNGVLNSWTDQD,KSFNRNEC,KTSTSPIVKSFNRNEC,NGVLNSWTDQDSK,NNFYPKDINVKWKID,VLNSWTDQDSKD,STSPIVKSF,DSTYSMSSTLT,INVKWKIDGSERQ,VKWKIDGSE,SKDSTYSMSSTLT,TCEATHKTSTSPIVKSF,NGVLNSWTDQDSKDSTYS,KTSTSPIVK,NFYPKDINVKW,GASVVCFLNNFYPKD,AAPTVSIFPPSSE,DINVKWKIDGSER,KDINVKW,NNFYPKDINVKW,ERHNSYTCE,TKDEYER,MSSTLTLTKDEYE,FLNNFYPKDIN,SKDSTYSMSST,KIDGSERQNGVLNSWTDQDSKDSTY,VLNSWTDQDSK,KTSTSPIVKSF,SMSSTLTLTK,ATHKTSTSPIVKS,TLTKDEYERHNSY,RQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE,NGVLNSWTDQDSKD,KIDGSERQN,STLTLTKDE,SKDSTYSMSSTL,SMSSTLTLTKDEYERHNSY,GVLNSWTDQDSKDSTYSMS,FYPKDINVKWKID,QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYER,LNNFYPKDINVKW,SVVCFLNNFYPKDINV,GVLNSWTDQDSKDSTYSMSSTLTLTKDEYE,SGGASVVCFLNNFYPKD,SWTDQDSKD,VKWKIDGSERQNGVL,SYTCEATHKTSTSPIVKSF,TKDEYERHNSYTCE,GVLNSWTDQDSK,SWTDQDSKDSTYSMS,GSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE,FLNNFYPKDINVKW,ATHKTSTSPIV,VSIFPPSSEQL,TSGGASVVCFLNNFYPK,IFPPSSEQLTSGGASVVCF,RQNGVLNS,DINVKWKIDGSERQ,WTDQDSKDSTYSMSSTL,SGGASVVCFLNNFYPK,STLTLTKDEYER,SKDSTYSMSSTLTLTKDE,QLTSGGASVVCFLNNFYPKD,TSTSPIVKSF,YPKDINVKWKIDGSERQNGVL,DSKDSTYSMSSTLT,TLTKDEYERHN,TLTLTKDEYE,NFYPKDINVKWK,HNSYTCEATHK,TLTKDEYER,IFPPSSEQL,SKDSTYSM,QLTSGGASVVCFL,SSTLTLTKDE,TLTLTKDEYER,SGGASVVCFLNNFYPKDINVKWKID,MSSTLTLTKDE,GVLNSWTDQDSKDSTY,STYSMSSTLTLTKDE,DSKDSTYSMSSTLTLTK,GVLNSWTDQDSKDSTYS,QNGVLNSWTDQDSKD,IDGSERQNGVLNSWTDQDSK,INVKWKIDGSE,NSWTDQDSKDSTY,WKIDGSERQNGVLNSWTDQDSK,RQNGVLNSWTDQDSKD,STYSMSSTLTLTKDEYE,SFNRNEC,WKIDGSER,DINVKWK,NSWTDQDSKDSTYSMSSTLT,WKIDGSE,YPKDINV,LNNFYPKDINVKWKID,TYSMSSTLTLTKDE,SSTLTLTKDEYER,ATHKTSTSPIVK,NNFYPKDINVKWKIDGSE,FLNNFYPKD,NSWTDQDSKDSTYSM,GVLNSWTDQDSKD,LNNFYPKDINV,GVLNSWTDQDSKDSTYSMSSTLTLTKDE,QNGVLNSWTDQDSKDSTYSMS,LNNFYPK,IFPPSSEQLTSGGAS,TCEATHKTSTSPIVK,ATHKTSTSPIVKSFNRNE,NSWTDQDSKDSTYSMS,KIDGSERQNGVL,SMSSTLTLTKDEYER,IDGSERQNGVLNSWTDQDS,QNGVLNSWTDQDSKDSTYSMSSTLTLTK,NFYPKDINVK,TYSMSSTLTLTKDEYER,FLNNFYPK,YPKDINVKWKIDGSE,SGGASVVCFLNNFYPKDINVK,NSWTDQDSKDSTYSMSSTLTLTKDEYER,DQDSKDSTYSMSSTLT,IFPPSSEQLT,MSSTLTLTKDEYER,RHNSYTCE,NSWTDQDSKDSTYSMSSTL,IDGSERQNGVLNSWTDQ,DAAPTVSIFPPSSEQLT,TSTSPIVK,WTDQDSKDSTYSM,LTLTKDEY,HNSYTCEATHKTSTSPIVK,RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPK,NNFYPKDINVK,RADAAPTVSIFPPSSEQLT,KTSTSPIVKSFN,NFYPKDINVKWKID,TSGGASVVCF,LNNFYPKDINVKWK,SWTDQDSKDSTYSMSSTLTLTKDE,GASVVCFLNNFYPKDINVK,LNNFYPKDINVKWKIDGSERQNGVL,LNNFYPKDIN,NSWTDQDSKDSTYSMSST,ATHKTSTSPIVKSFNRNEC,GGASVVCFLNNFYPK,STYSMSSTLT,DSTYSMSSTLTLTKDEYER,NSWTDQDSKDST,NGVLNSWTDQDSKDSTY,STLTLTKDEYE,INVKWKID,CFLNNFYPKDINVKW,LNNFYPKD,NGVLNSWTDQDS,LNNFYPKDINVK,ADAAPTVSIFPPSSEQLT,STYSMSSTLTLTKDEYER,YPKDINVKWKIDG,GVLNSWTDQD,QNGVLNSWTDQDSK,MSSTLTLTK,SMSSTLTLTKDEYE,LNNFYPKDI,GSERQNGVLNSWTDQDSKD,LNNFYPKDINVKWKIDGSE,DSTYSMSSTLTLTK,IDGSERQNGVLNSWTDQDSKD,TSTSPIVKSFNRNEC,GASVVCFLNNFYPK,DSKDSTYSMSSTL,NFYPKDINVKWKIDGSE,NSWTDQDSK,NGVLNSWTDQD,LTKDEYER,NSWTDQDSKD,TDQDSKDSTY,TSTSPIVKSFN,IFPPSSEQLTSGGASVVCFLNNFYPK,SYTCEATHK
  Total Peptides: 182
# Num Classes: 3
# Unique Peptides: 744
# Final Seq: DIVMSQSPSSIAVSVGEKVTMSCKSSQSIIYSSNQKNYIAWYQQKPGQSPKIIIYWASTRESGVPDRFTGSGSGTDFTITISSVKAEDIAVYYCQQYYSYPRTFGGGTQIEIKR-RADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
# Sitewise Support: -79 82 82 82 94 98 101 101 101 99 102 109 106 105 105 105 105 85 33 31 29 14 14 14 20 20 20 20 20 18 12 8 8 8 10 9 9 9 13 17 17 24 24 24 25 29 29 29 29 29 31 51 52 54 53 53 52 52 52 52 1 3 3 3 3 3 3 25 25 26 26 26 26 26 26 26 31 34 35 37 36 36 36 36 36 15 15 12 10 4 9 7 7 5 5 7 7 8 8 9 4 3 10 15 18 17 18 19 20 20 19 15 15 3 -5 6 9 12 12 12 12 14 14 32 32 32 32 32 32 32 32 32 32 42 43 50 50 51 49 49 50 57 84 89 99 100 106 106 108 73 70 69 69 65 65 53 58 58 56 55 55 50 64 74 86 88 88 103 106 109 118 119 119 123 122 119 144 162 165 163 158 162 163 166 171 168 162 162 164 164 126 126 76 76 67 32 32 34 34 42 42 42 53 53 53 65 53 54 56 56 56 56 56 65 51 49 36 32 32 32 31 
# Sitewise Overlap: -79 82 82 82 94 98 101 101 101 99 102 109 106 105 105 105 105 85 33 31 29 14 14 14 20 20 20 20 20 18 12 8 8 8 10 9 9 9 13 17 17 24 24 24 25 29 29 29 29 29 31 51 52 54 53 53 52 52 52 52 1 3 3 3 3 3 3 25 25 26 26 26 26 26 26 26 31 34 35 37 36 36 36 36 36 15 15 12 10 4 9 7 7 7 7 7 10 9 9 10 9 9 11 16 20 20 20 20 20 20 19 16 16 3 -5 6 9 12 12 12 12 14 14 32 32 32 32 32 32 32 32 32 32 42 43 50 50 51 49 49 50 57 84 89 99 100 106 106 108 73 70 69 69 65 65 53 58 58 56 55 55 50 64 74 86 88 88 103 106 109 118 119 119 123 122 119 144 162 165 163 158 162 163 166 171 168 162 162 164 164 126 126 76 76 67 32 32 34 34 42 42 42 53 53 53 65 53 54 56 56 56 56 56 65 51 49 36 32 32 32 31 
# FinalLen: 221
# % Correct: 0.0