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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.<\/jats:p>","DOI":"10.1073\/pnas.0701130104","type":"journal-article","created":{"date-parts":[[2007,4,3]],"date-time":"2007-04-03T01:04:22Z","timestamp":1175562262000},"page":"6140-6145","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":144,"title":["Protein identification by spectral networks analysis"],"prefix":"10.1073","volume":"104","author":[{"given":"Nuno","family":"Bandeira","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dekel","family":"Tsur","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, 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