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Molecular & Cellular Proteomics 8:53-69, 2009.
© 2009 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Spectral Dictionaries

Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra ^*,S

Sangtae Kim, Nitin Gupta, Nuno Bandeira and Pavel A. Pevzner^,,¶

From the Department of Computer Science and Engineering and Bioinformatics Program, University of California San Diego, La Jolla, California 92093

Database search tools identify peptides by matching tandem mass spectra against a protein database. We study an alternative approach when all plausible de novo interpretations of a spectrum (spectral dictionary) are generated and then quickly matched against the database. We present a new MS-Dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that MS-Dictionary can identify spectra that are missed in the database search. We argue that MS-Dictionary enables proteogenomics searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches. We show that such searches allow one to correct sequencing errors and find programmed frameshifts.

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This article has been cited by other articles:

				S. Kim, N. Bandeira, and P. A. Pevzner Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification Mol. Cell. Proteomics, June 1, 2009; 8(6): 1391 - 1400. [Abstract] [Full Text] [PDF]