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Mol Cell Proteomics. 2011 Nov;10(11):R111.009522. doi: 10.1074/mcp.R111.009522. Epub 2011 Aug 29.

A face in the crowd: recognizing peptides through database search.

Author information

1
University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA. engj@u.washington.edu

Abstract

Peptide identification via tandem mass spectrometry sequence database searching is a key method in the array of tools available to the proteomics researcher. The ability to rapidly and sensitively acquire tandem mass spectrometry data and perform peptide and protein identifications has become a commonly used proteomics analysis technique because of advances in both instrumentation and software. Although many different tandem mass spectrometry database search tools are currently available from both academic and commercial sources, these algorithms share similar core elements while maintaining distinctive features. This review revisits the mechanism of sequence database searching and discusses how various parameter settings impact the underlying search.

PMID:
21876205
PMCID:
PMC3226415
DOI:
10.1074/mcp.R111.009522
[Indexed for MEDLINE]
Free PMC Article
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