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    Mol Cell Proteomics. 2009 Jan;8(1):53-69. Epub 2008 Aug 14.

    Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.

    Kim S, Gupta N, Bandeira N, Pevzner PA.

    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

    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.

    PMID: 18703573 [PubMed - indexed for MEDLINE]

    PMCID: 2621003

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