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Mol Cell Proteomics. 2012 Apr;11(4):M111.010587. doi: 10.1074/mcp.M111.010587. Epub 2011 Dec 20.

PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.

Author information

1
Bioinformatics Solutions Inc., Waterloo, Ontario N2L 6J2, Canada.

Abstract

Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. PEAKS DB achieves significantly improved accuracy and sensitivity over two other commonly used software packages. Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of overconfidence that exists in the conventional target decoy method for certain types of peptide identification software.

PMID:
22186715
PMCID:
PMC3322562
DOI:
10.1074/mcp.M111.010587
[Indexed for MEDLINE]
Free PMC Article

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