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 pattern 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.

CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

“…Although distinguishing of a linear and a cyclic peptide spectrum has been proposed for Figure 5. The theoretical T-peptide spectrum was compared with its experimental one ribosomal peptides [5], distinguishing various types of NRPs is still a nontrivial task. It may be advantageous to run the engine repeatedly for different types of NRPs.…”

Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra

“…While databases in traditional proteomics consist of known peptides, the ongoing genome mining efforts for PNP discovery 35 generate vast databases of still uncharacterized putative PNPs 7, 42, 43 . Since predicting an NRP encoded by an NRPS is a difficult problem, various tools for predicting specificities of A-domains 44 output multiple rather than a single candidate amino acid for each A-domain.…”

Mass spectrometry of natural products: current, emerging and future technologies

“…In principle, metabolomics databases that allow one to search based on an MS and/or MS/MS patterns such as Massbank 87 , Metlin 88 , NIST 89 , LIPIDMAPS 90 (Table 1) could be consulted, but these databases are rarely consulted because there are few NPs present in the databases. Emerging de novo informatics tools can predict fragmentation data from imported structures or partial structures and then match it to the experimental fragmentation spectra Such approaches are aiding in the dereplication of certain subclasses of ribosomally-synthesized and post-translationally-modified peptides NPs 91 , non-ribosomal peptides 91-94 , and lipids 95 (Table 2). …”

“…The structural prediction of such cyclic peptides is enhanced by the use of fragmentation trees. Additional tools to de novo predict cyclic peptides continue to be developed 91, 109 . More recently the de novo structure prediction has been extended to other structural classes of NPs with fragmentation trees 110 .…”