title: Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases.
abstract: 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.
authors.affiliation: Department of Electrical and Computer Engineering, University of California, San Diego, California, United States.
authors.forename: Hosein
authors.initials: H
authors.lastname: Mohimani
authors.forename: Wei-Ting
authors.initials: WT
authors.lastname: Liu
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Mylne
authors.forename: Aaron G
authors.initials: AG
authors.lastname: Poth
authors.forename: Michelle L
authors.initials: ML
authors.lastname: Colgrave
authors.forename: Dat
authors.initials: D
authors.lastname: Tran
authors.forename: Michael E
authors.initials: ME
authors.lastname: Selsted
authors.forename: Pieter C
authors.initials: PC
authors.lastname: Dorrestein
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000818:Animals; D001412:Bacillus subtilis / Q000378:metabolism; D001894:Borohydrides / Q000737:chemistry; D030541:Databases, Genetic; D023082:Defensins / Q000737:chemistry; D016678:Genome; D006368:Helianthus / Q000378:metabolism; D008253:Macaca mulatta; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D012270:Ribosomes / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry / Q000379:methods; D014357:Trypsin / Q000737:chemistry
chemical_list: D001894:Borohydrides; D023082:Defensins; D010455:Peptides; C450142:theta-defensin; C025364:sodium borohydride; D014357:Trypsin