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

TitleSpectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.
Publication TypeJournal Article
Year of Publication2009
AuthorsKim S, Gupta N, Bandeira N, Pevzner PA
JournalMol Cell Proteomics
Volume8
Issue1
Pagination53-69
Date Published2009 Jan
ISSN1535-9484
KeywordsAlgorithms, Amino Acid Sequence, Databases, Protein, Genome, Human, Humans, Molecular Sequence Data, Peptides, Sequence Analysis, Protein, Shewanella, Tandem Mass Spectrometry
Abstract

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.

DOI10.1074/mcp.M800103-MCP200
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18703573?dopt=Abstract
PMCPMC2621003
Alternate TitleMol. Cell Proteomics
PubMed ID18703573