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

Eng JK, Searle BC, Clauser KR, Tabb DL
Mol Cell Proteomics. 2011 10 (11): R111.009522

PMID: 21876205 · PMCID: PMC3226415 · DOI:10.1074/mcp.R111.009522

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.

MeSH Terms (11)

Algorithms Amino Acid Sequence Animals Databases, Protein Humans Molecular Weight Peptide Fragments Protein Processing, Post-Translational Proteome Search Engine Tandem Mass Spectrometry

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