title: Protein identification by spectral networks analysis.
abstract: Advances in tandem mass spectrometry (MS/MS) steadily increase the rate of generation of MS/MS spectra. As a result, the existing approaches that compare spectra against databases are already facing a bottleneck, particularly when interpreting spectra of modified peptides. Here we explore a concept that allows one to perform an MS/MS database search without ever comparing a spectrum against a database. We propose to take advantage of spectral pairs, which are pairs of spectra obtained from overlapping (often nontryptic) peptides or from unmodified and modified versions of the same peptide. Having a spectrum of a modified peptide paired with a spectrum of an unmodified peptide allows one to separate the prefix and suffix ladders, to greatly reduce the number of noise peaks, and to generate a small number of peptide reconstructions that are likely to contain the correct one. The MS/MS database search is thus reduced to extremely fast pattern-matching (rather than time-consuming matching of spectra against databases). In addition to speed, our approach provides a unique paradigm for identifying posttranslational modifications by means of spectral networks analysis.
authors.affiliation: Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA. bandeira@cs.ucsd.edu
authors.forename: Nuno
authors.initials: N
authors.lastname: Bandeira
authors.forename: Dekel
authors.initials: D
authors.lastname: Tsur
authors.forename: Ari
authors.initials: A
authors.lastname: Frank
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins