Journal
MOLECULAR & CELLULAR PROTEOMICS
Volume 8, Issue 1, Pages 53-69Publisher
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
DOI: 10.1074/mcp.M800103-MCP200
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Funding
- National Institutes of Health [5R01RR016522-05]
- Howard Hughes Medical Institute professor award
- NATIONAL CENTER FOR RESEARCH RESOURCES [R01RR016522] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P41GM103484] Funding Source: NIH RePORTER
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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. Molecular & Cellular Proteomics 8:53-69, 2009.
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