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.
run 'cmake .' and then run 'make'
Windows users should try our webserver at cyclo.ucsd.edu.
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
A powerful tool for PTM discovery (Jan 2008, Journal of Proteome research, Vol 7. Issue 1)
From spectral networks to shotgun sequencing (June 2007, Nature Methods, Vol. 4 No. 6)
Identifying peptides without a database (May 2007, Journal of Proteome Research)
UCSD Computer Scientist Wins Young Investigator Award, Research on Snake Venom Proteins Highlighted (Nov 2006, UCSD)