Center for Computational Mass Spectrometry

Publications

Publications co-authored by CCMS members.

Published in 2020

    MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets
    Meena Choi, Jeremy Carver, [...], Nuno Bandeira, Olga Vitek. "MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets", Nat Methods 2020 Oct;17(10):981-984 32929271.

Published in 2016

    Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
    Mingxun Wang, Jeremy J Carver, [...], Pieter C Dorrestein, Nuno Bandeira. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature biotechnology 34.8 (2016): 828-837 27504778.
    Lifestyle chemistries from phones for individual profiling
    Amina Bouslimani, Alexey V Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein. "Lifestyle chemistries from phones for individual profiling." Proceedings of the National Academy of Sciences 113.48 (2016): E7645-E7654. 27849584.

Published in 2015

    Advanced proteogenomic analysis reveals multiple peptide mutations and complex immunoglobulin peptides in colon cancer
    Woo, S.; Cha, S. W.;,Bonissone, S.; et al. J Proteome Res. 2015. In press
    Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer
    26139413.
    Molecular cartography of the human skin surface in 3D
    Amina Bouslimani, Carla Porto, Christopher M Rath, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W Borkowski, Michael J Meehan, Kathleen Dorrestein, Richard L Gallo, Nuno Bandeira, Rob Knight, Theodore Alexandrov, Pieter C Dorrestein. "Molecular cartography of the human skin surface in 3D." Proceedings of the National Academy of Sciences 112.17 (2015): E2120-E2129. 25825778 .

Published in 2014

    Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms.
    Terterov I, Vyatkina K, Kononikhin AS, Boitsov V, Vyazmin S, Popov IA, Nikolaev EN, Pevzner P, Dubina M.
    Rapid Commun Mass Spectrom. 2014 Jan 15;28(1):33-41. doi: 10.1002/rcm.6757.     24285388.
    The generating function approach for peptide identification in spectral networks
    Guthals A., Christina B. Bandeira N. Research in Computational Molecular Biology, Lecture Notes in Computer Science; (8394) 85-99 MSV000078529.
    An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays.
    Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. Mol Cell Proteomics. 2014 Jan;13(1):157-67. doi: 10.1074/mcp.M113.031260. Epub 2013 Oct 18. 24142994.
    MixGF: spectral probabilities for mixture spectra from more than one peptide
    Wang, J., Bourne, P. E., & Bandeira, N. (2014). MixGF: spectral probabilities for mixture spectra from more than one peptide. Molecular & Cellular Proteomics, mcp-O113.037218 PMID:25225354.
    Proteogenomic database construction driven from large scale RNA-seq data
    Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. J Proteome Res. 2014 Jan 3;13(1):21-8. doi: 10.1021/pr400294c. Epub 2013 Jul 17. 23802565.
    A Turn-key Approach for Large-scale Identification of Complex Post-translational Modifications
    Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. J Proteome Res. 2014 Mar 7;13(3):1190-9. doi: 10.1021/pr400368u. Epub 2014 Jan 29. 24437954.
    Combinatorial Approach for Large-scale Identification of Linked Peptides from MS/MS Spectra
    Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. Mol Cell Proteomics. 2014 Apr;13(4):1128-36. doi: 10.1074/mcp.M113.035758. Epub 2014 Feb 3. 24493012.
    Expanding proteome coverage with orthogonal-specificity α-lytic proteases.
    Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. Mol Cell Proteomics. 2014 Mar;13(3):823-35. doi: 10.1074/mcp.M113.034710. Epub 2014 Jan 14. 24425750.
    Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.
    Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX. Mol Cell Proteomics. 2014 Jan;13(1):360-71. doi: 10.1074/mcp.M113.032813. Epub 2013 Oct 31. 24187338.
    Universal tool for MS/MS database search.
    Kim S., Pevzner PA. In preparation.
    MS-GF+ makes progress towards a universal database search tool for proteomics.
    Kim S, Pevzner PA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun. 2014 Oct 31;5:5277. 25358478 .
    Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data
    Woo, S.; Cha, S. W.; et al., PROTEOMICS. 2014 Dec;14(23-24):2719-30. doi: 10.1002/pmic.201400206. Epub 2014 Nov 17. 25263569.

Published in 2013

    Identification of ultramodified proteins using top-down tandem mass spectra.
    Liu X, Hengel S, Wu S, Tolić N, Pasa-Tolić L, Pevzner PA. J Proteome Res. 2013 Dec 6;12(12):5830-8. doi: 10.1021/pr400849y. Epub 2013 Nov 15. 24188097.
    UniNovo: a universal tool for de novo peptide sequencing.
    Jeong K, Kim S, Pevzner PA. Bioinformatics. 2013 Aug 15;29(16):1953-62. doi: 10.1093/bioinformatics/btt338. Epub 2013 Jun 12. 23766417, PMC3722526. MSV000078533.
    Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.
    Guthals A, Clauser KR, Frank AM, Bandeira N. J Proteome Res. 2013 Jun 7;12(6):2846-57. 23679345. MSV000078436.
    MS/MS networking guided analysis of molecule and gene cluster families.
    Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):E2611-20. doi: 10.1073/pnas.1303471110. Epub 2013 Jun 24.
     23798442, PMC3710860.
    Spectral library generating function for assessing spectrum-spectrum match significance.
    Wang M, Bandeira N. J Proteome Res. 2013 Sep 6;12(9):3944-51. doi: 10.1021/pr400230p. Epub 2013 Jul 31. 23808827, PMC3766387. MSV000078519.
    N-terminal protein processing: a comparative proteogenomic analysis.
    Bonissone S, Gupta N, Romine M, Bradshaw RA, Pevzner PA. Mol Cell Proteomics. 2013 Jan;12(1):14-28. doi: 10.1074/mcp.M112.019075. Epub 2012 Sep 23. 23001859, PMC3536895.
    A New Approach to Evaluating Statistical Significance of Spectral Identifications.
    Mohimani H, Kim S, Pevzner PA. J Proteome Res. 2013 Apr 5;12(4):1560-8. doi: 10.1021/pr300453t. Epub 2013 Mar 8. 23343606. Link.
    Neutron-encoded signatures enable product ion annotation from tandem mass spectra.
    Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, Coon JJ. Mol Cell Proteomics. 2013 Dec;12(12):3812-23. 24043425.
    Top-down proteomics reveals a unique protein s-thiolation switch in the bacterial pathogen salmonella in response to infection-like conditions
    C. Ansong, S. Wu, M. Da, X. Liu, H. Brewer, L. Brooke, D. Kaiser, Nakayasu E.S., P.A. Cort, J.R.and Pevzner, R.D. Smith, F. Heffron, J.N. Adkins, and L. Pasa-Tolic. Proc Natl Acad Sci U S A, 110:10153--8, 2013. 23720318.
    How many signal peptides are there in bacteria?
    Ivankov D.N. , Payne S.H., Galperin M.Y., Bonissone S., Pevzner P.A., Frishman D. Environ Microbiol., 15:983–90, 2013. PMID:23556536.

Published in 2012

    Interkingdom metabolic transformations captured by microbial imaging mass spectrometry.
    Moree WJ, Phelan VV, Wu CH, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13811-6. doi: 10.1073/pnas.1206855109. 22869730, PMC3427086 .
    Protein identification using top-down.
    Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524. Epub 2011 Oct 25. 22027200, PMC3433905 .
    Speeding up tandem mass spectral identification using indexes.
    Liu X, Mammana A, Bafna V. Bioinformatics. 2012 Jul 1;28(13):1692-7. doi: 10.1093/bioinformatics/bts244. Epub 2012 Apr 27. 22543365, PMC3381964 .
    Fast multi-blind modification search through tandem mass spectrometry.
    Na S, Bandeira N, Paek E. Mol Cell Proteomics. 2012 Apr;11(4):M111.010199. doi: 10.1074/mcp.M111.010199. Epub 2011 Dec 20. 22186716, PMC3322561 . MSV000078532.
    Accurate mass spectrometry based protein quantification via shared peptides.
    Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. J Comput Biol. 2012 Apr;19(4):337-48. doi: 10.1089/cmb.2009.0267. Epub 2012 Mar 13. 22414154, PMC3317402 .
    Mass spectral molecular networking of living microbial colonies.
    Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1743-52. doi: 10.1073/pnas.1203689109. Epub 2012 May 14. 22586093, PMC3387089 .
    Peptide identification by tandem mass spectrometry with alternate fragmentation modes.
    Guthals A, Bandeira N. Mol Cell Proteomics. 2012 Sep;11(9):550-7. 22595789.
    Shotgun protein sequencing with meta-contig assembly.
    Guthals A, Clauser KR, Bandeira N. Mol Cell Proteomics. 2012 Oct;11(10):1084-96. 22798278, PMC3494147. MSV000078530.
    False discovery rates in spectral identification.
    Jeong K, Kim S, Bandeira N. BMC Bioinformatics. 2012;13 Suppl 16:S2. doi: 10.1186/1471-2105-13-S16-S2. Epub 2012 Nov 5. 23176207, PMC3489529. Link.
    The spectral networks paradigm in high throughput mass spectrometry.
    Guthals A, Watrous JD, Dorrestein PC, Bandeira N. Mol Biosyst. 2012 Oct;8(10):2535-44. 22610447.
    Unexpected diversity of signal peptides in prokaryotes.
    Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolić L, Smith RD, Pevzner PA. MBio. 2012 Nov 20;3(6). pii: e00339-12. doi: 10.1128/mBio.00339-12. 23169999.
    Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes.
    Choi S, Srivas R, Fu KY, Hood BL, Dost B, Gibson GA, Watkins SC, Van Houten B, Bandeira N, Conrads TP, Ideker T, Bakkenist CJ. J Proteome Res. 2012 Oct 5;11(10):4983-91. doi: 10.1021/pr3005524. Epub 2012 Sep 18. 22909323.

Published in 2011

    Protein identification by spectral networks analysis.
    Bandeira N. Methods Mol Biol. 2011;694:151-68. doi: 10.1007/978-1-60761-977-2_11. 21082434 .
    Gapped spectral dictionaries and their applications for database searches of tandem mass spectra.
    Jeong K, Kim S, Bandeira N, Pevzner PA. Mol Cell Proteomics. 2011 Jun;10(6):M110.002220. doi: 10.1074/mcp.M110.002220. Epub 2011 Mar 28. 21444829, PMC3108828.
    Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra
    Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. Nat Methods. 2011 May 15;8(7):587-91. doi: 10.1038/nmeth.1609. 21572408, PMC3128193 .
    Connecting chemotypes and phenotypes of cultured marine microbial assemblages by imaging mass spectrometry.
    Yang YL, Xu Y, Kersten RD, Liu WT, Meehan MJ, Moore BS, Bandeira N, Dorrestein PC.
    Angew Chem Int Ed Engl. 2011 Jun 20;50(26):5839-42. doi: 10.1002/anie.201101225. Epub 2011 May 13.     21574228, PMC3687529.
    Advancing next-generation proteomics through computational research.
    Bandeira N, Nesvizhskii A, McIntosh M. J Proteome Res. 2011 Jul 1;10(7):2895. doi: 10.1021/pr200484b. Epub 2011 May 31. 21627070 .
    NeuroPedia: neuropeptide database and spectral library.
    Kim Y, Bark S, Hook V, Bandeira N. Bioinformatics. 2011 Oct 1;27(19):2772-3. doi: 10.1093/bioinformatics/btr445. Epub 2011 Aug 5. 21821666, PMC3179654 .
    Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody.Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody.
    Castellana NE, McCutcheon K, Pham VC, Harden K, Nguyen A, Young J, Adams C, Schroeder K, Arnott D, Bafna V, Grogan JL, Lill JR. Proteomics. 2011 Feb;11(3):395-405. doi: 10.1002/pmic.201000487. Epub 2011 Jan 5. 21268269, PMC3253889 .
    Peptide identification by database search of mixture tandem mass spectra.
    Wang J, Bourne PE, Bandeira N. Mol Cell Proteomics. 2011 Dec;10(12):M111.010017. doi: 10.1074/mcp.M111.010017. Epub 2011 Aug 23. 21862760.
    Automated querying and identification of novel peptides using MALDI mass spectrometric imaging.
    Bruand J, Sistla S, Mériaux C, Dorrestein PC, Gaasterland T, Ghassemian M, Wisztorski M, Fournier I, Salzet M, Macagno E, Bafna V. J Proteome Res. 2011 Apr 1;10(4):1915-28. doi: 10.1021/pr101159e. Epub 2011 Mar 15. 21332220 .
    AMASS: algorithm for MSI analysis by semi-supervised segmentation.
    Bruand J, Alexandrov T, Sistla S, Wisztorski M, Meriaux C, Becker M, Salzet M, Fournier I, Macagno E, Bafna V. J Proteome Res. 2011 Oct 7;10(10):4734-43. doi: 10.1021/pr2005378. Epub 2011 Aug 25. 21800894, PMC3190602 .
    Sequencing cyclic peptides by multistage mass spectrometry.
    Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA. Proteomics. 2011 Sep;11(18):3642-50. doi: 10.1002/pmic.201000697. Epub 2011 Aug 9. 21751357, PMC3398611.
    Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases.
    Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner PA. J Proteome Res. 2011 Oct 7;10(10):4505-12. doi: 10.1021/pr200323a. Epub 2011 Sep 7. 21851130, PMC3242011 .
    Multiplex de novo sequencing of peptide antibiotics.
    Mohimani H, Liu WT, Yang YL, Gaudêncio SP, Fenical W, Dorrestein PC, Pevzner PA. J Comput Biol. 2011 Nov;18(11):1371-81. doi: 10.1089/cmb.2011.0158. Epub 2011 Oct 28. 22035290, PMC3216106.
    Target-decoy approach and false discovery rate: when things may go wrong.
    Gupta N, Bandeira N, Keich U, Pevzner PA. J Am Soc Mass Spectrom. 2011 Jul;22(7):1111-20. doi: 10.1007/s13361-011-0139-3. Epub 2011 May 5. 21953092, PMC3220955.
    Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage
    Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH. PLoS One. 2011 Apr 12;6(4):e18565. doi: 10.1371/journal.pone.0018565. 21533272.
    Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes
    Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA. Genome Res. 2008 Jul;18(7):1133-42. doi: 10.1101/gr.074344.107. Epub 2008 Apr 21. 18426904.
    Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera
    Mevers E, Liu WT, Engene N, Mohimani H, Byrum T, Pevzner PA, Dorrestein PC, Spadafora C, Gerwick WH. J Nat Prod. 2011 May 27;74(5):928-36. doi: 10.1021/np200077f. Epub 2011 Apr 13. 21488639.

Published in 2010

    Peptide identification from mixture tandem mass spectra.
    Wang J, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N. Mol Cell Proteomics. 2010 Jul;9(7):1476-85. doi: 10.1074/mcp.M000136-MCP201. Epub 2010 Mar 27. 20348588, PMC2938093 .
    Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum.
    Gonzalez DJ, Lee SW, Hensler ME, Markley AL, Dahesh S, Mitchell DA, Bandeira N, Nizet V, Dixon JE, Dorrestein PC. J Biol Chem. 2010 Sep 3;285(36):28220-8. doi: 10.1074/jbc.M110.118554. Epub 2010 Jun 25. 2058111, PMC2934687 .
    Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication.
    Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. AAPS J. 2010 Dec;12(4):635-45. doi: 10.1208/s12248-010-9223-z. Epub 2010 Aug 24. 20734175, PMC2976990.
    Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry.
    Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner PA. Proteomics. 2010 Aug;10(15):2833-44. doi: 10.1002/pmic.200900821. 20597098, PMC3220954 .
    Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing.
    Gupta N, Bark SJ, Lu WD, Taupenot L, O'Connor DT, Pevzner P, Hook V. J Proteome Res. 2010 Oct 1;9(10):5065-75. doi: 10.1021/pr100358b.
     20704348, PMC3000314.
    Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis.
    Liu WT, Yang YL, Xu Y, Lamsa A, Haste NM, Yang JY, Ng J, Gonzalez D, Ellermeier CD, Straight PD, Pevzner PA, Pogliano J, Nizet V, Pogliano K, Dorrestein PC. Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16286-90. doi: 10.1073/pnas.1008368107. Epub 2010 Aug 30. 20805502, PMC2941286 .
    Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.
    Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. Mol Cell Proteomics. 2010 Dec;9(12):2772-82. doi: 10.1074/mcp.M110.002766. Epub 2010 Sep 20. 20855543, PMC310195 .
    The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search
    Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. Mol Cell Proteomics. 2010 Dec;9(12):2840-52. doi: 10.1074/mcp.M110.003731. Epub 2010 Sep 9. 20829449, PMC3101864. MSV000078533.
    Template proteogenomics: sequencing whole proteins using an imperfect database.
    Castellana NE, Pham V, Arnott D, Lill JR, Bafna V. Mol Cell Proteomics. 2010 Jun;9(6):1260-70. doi: 10.1074/mcp.M900504-MCP200. Epub 2010 Feb 17.
     20164058.
    Synergistic allelochemicals from a freshwater cyanobacterium
    P.N. Leao, A.R. Pereirab, W.T. Liu, J. Ng, P.A. Pevzner, P.C. Dorrestein, G.M. Konig, M. Teresa, S.D. Vasconcelos, V.M. Vasconcelos, and W.H. Gerwick. Proc. Nat. Acad Sciences, 107(25):11183--8, 2010. PMC2895120.
    Proteogenomics to discover the full coding content of genomes: a computational perspective
    Castellana N, Bafna V. J Proteomics. 2010 Oct 10;73(11):2124-35. doi: 10.1016/j.jprot.2010.06.007. Epub 2010 Jul 8. 20620248.

Published in 2009

    Spectral dictionaries integrating de novo peptide sequencing with database search of tandem mass spectra.
    Kim S, Gupta N, Bandeira N, Pevzner PA. Mol Cell Proteomics. 2009 Jan;8(1):53-69. doi: 10.1074/mcp.M800103-MCP200. Epub 2008 Aug 14. 18703573.
    Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification
    Kim S, Bandeira N, Pevzner PA. Mol Cell Proteomics. 2009 Jun;8(6):1391-400. doi: 10.1074/mcp.M800535-MCP200. Epub 2009 Mar 2. 19254948.
    Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides
    Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. Anal Chem. 2009 Jun 1;81(11):4200-9. doi: 10.1021/ac900114t. 19413302.
    Dereplication and de novo sequencing of nonribosomal peptides
    Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. Nat Methods. 2009 Aug;6(8):596-9. doi: 10.1038/nmeth.1350. Epub 2009 Jul 13. 19597502.
    Predicting intensity ranks of peptide fragment ions.
    Frank AM. J. Proteome Res., 8:2226–40, 2009. 19256476.
    A ranking-based scoring function for peptide-spectrum matches.
    Frank, AM. J. Proteome Res., 8:2241–52, 2009. 19231891.

Published in 2008

    Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.
    Kim S, Gupta N, Pevzner PA. J Proteome Res. 2008 Aug;7(8):3354-63. doi: 10.1021/pr8001244. Epub 2008 Jul 3. 18597511.
    Interpreting top-down mass spectra using spectral alignment
    Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA. Anal Chem. 2008 Apr 1;80(7):2499-505. doi: 10.1021/ac702324u. Epub 2008 Feb 27. 18302345.
    Automated de novo protein sequencing of monoclonal antibodies.
    Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR. Nat Biotechnol. 2008 Dec;26(12):1336-8. 19060866.
    Clustering millions of tandem mass spectra.
    Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. J Proteome Res. 2008 Jan;7(1):113-22. Epub 2007 Dec 8. 18067247.
    Multi-spectra peptide sequencing and its applications to multistage mass spectrometry.
    Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. Bioinformatics. 2008 Jul 1;24(13):i416-23. 18785330.
    Accurate annotation of peptide modifications through unrestrictive database search
    Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. J Proteome Res. 2008 Jan;7(1):170-81. Epub 2007 Nov 23. 18034453.
    Does trypsin cut before proline?
    Rodriguez J, Gupta N, Smith RD, Pevzner PA. J Proteome Res. 2008 Jan;7(1):300-5. Epub 2007 Dec 8. 18067249.

Published in 2007

    Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.
    Bandeira N, Clauser KR, Pevzner PA. Mol Cell Proteomics. 2007 Jul;6(7):1123-34. 17446555.
    Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications.
    Bandeira N. Biotechniques. 2007 Jun;42(6):687, 689, 691 passim. 17612289.
    Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.
    Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Genome Res. 2007 Sep;17(9):1362-77. Epub 2007 Aug 9. 17690205.
    Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing.
    Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. Proteomics. 2007 Jul;7(14):2318-29. 17623296.
    Protein identification by spectral networks analysis.
    Bandeira N, Tsur D, Frank A, Pevzner PA. Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6140-5. Epub 2007 Apr 2. 17404225.
    De novo peptide sequencing and identification with precision mass spectrometry.
    Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA. J Proteome Res. 2007 Jan;6(1):114-23. 17203955.

Published in 2005

    PepNovo: de novo peptide sequencing via probabilistic network modeling.
    Frank, A., & Pevzner, P. Anal Chem. 2005 77(4), 964-973.

Published in 2004

    Shotgun protein sequencing by tandem mass spectra assembly.
    Bandeira N, Tang H, Bafna V, Pevzner P. Anal Chem. 2004 Dec 15;76(24):7221-33. 15595863.