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National Academy of Sciences, Proceedings of the National Academy of Sciences, 15(104), p. 6140-6145, 2007

DOI: 10.1073/pnas.0701130104

Humana Press, Methods in Molecular Biology, p. 151-168, 2010

DOI: 10.1007/978-1-60761-977-2_11

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Protein identification by spectral networks analysis

Journal article published in 2007 by Dekel Tsur, Ari Frank, Pavel A. Pevzner, Nuno Bandeira
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.