Cycloquest

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Contact: Hosein Mohimani [hmohiman (at) ucsd.edu]

Summary

Cycloquest: Identification of Cyclopeptides via Database Search of Their Mass Spectra against Genome Databases.

Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computational techniques for cyclopeptide identification are still in their infancy, with many such peptides remaining uncharacterized. Tandem mass spectrometry has occupied a niche role in cyclopeptide identification, taking over from traditional techniques such as nuclear magnetic resonance spectroscopy (NMR). MS/MS studies require only picogram quantities of peptide (compared to milligrams for NMR studies) and are applicable to complex samples, abolishing the requirement for time-consuming chromatographic purification. While database search tools such as Sequest and Mascot have become standard tools for the MS/MS identification of linear peptides, they are not applicable to cyclopeptides, due to the parent mass shift resulting from cyclization and different fragmentation patterns of cyclic peptides. In this paper, we describe the development of a novel database search methodology to aid in the identification of cyclopeptides by mass spectrometry and evaluate its utility in identifying two peptide rings from Helianthus annuus, a bacterial cannibalism factor from Bacillus subtilis, and a θ-defensin from Rhesus macaque. The method is available online at cyclo.ucsd.edu.

Documentation

• Linux Installation
  
  run 'cmake .' and then run 'make'
  Windows users should try our webserver at cyclo.ucsd.edu.
  
  
• Run
  
  cycloquest_html : database search for linear/cyclic peptides
  
  The only required parameters of cycloquest are address of mgf/mzxml file, and fasta file. the parameters are described below:
  
  

  Required arguments:
  -------------------
  <path to input mzxml/mgf file>
  <path to input fasta file>
  
  Optional cycloquest_html arguments: 
  -----------------------------
  -out <path to output html file>                   (default : out.html)
  -linear                                search only for linear peptides
  -cyclic                                search only for cyclic peptides
  -num_top X            number of top search hits returned (default: 20)
  -num_peaks X                       number of top peaks kept in spectra 
  -parent_mass X       Parent Mass in Da (Default : from mzxml/mgf file)
  -charge                                (Default : from mzxml/mgf file)
  -add_decoy                                             search decoy DB
  -precursor_ion_tolerance                              Default : 0.5 Da
  -product_ion_tolerance                                Default : 0.5 Da
  -scan_num X                                Default : analyze all scans
  -filter_parent_mass X Y                  only analyze the species with
                                           parent mass between X and Y
  -num_cys X                       only accept peptides with X cysteines
  -reduced     	                        		                          	 
  -IAM_reduced
  -MAL_reduced
  -PFA_reduced
  -NaBH4_reduced
  -CMet_reduced
  -NIPIA_reduced