Technological Innovation and Resources
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification*
PEAKS DB: De novo Assisted Database Search

https://doi.org/10.1074/mcp.M111.010587Get rights and content
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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.

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This work was supported in part by the funds from Natural Sciences and Engineering Research Council of Canada Discovery program (to B. M. and G. L.) and by Bioinformatics Solutions Inc. (to J. Z., L. X., B. S., W. C., M. X., D. Y., W. Z., and Z. Z.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

This article contains supplemental material.