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.
Highlights
Innovations in tandem mass spectrometry (MS/MS)1 have enabled the rapid growth of proteomics for chemists and biologists alike
Researchers new to the field can benefit from a review of the fundamentals of tandem mass spectrometry sequence database searching, and even experienced proteomics researchers may profit from considerations of practical strategies to maximize information extraction from data
In a tandem mass spectrometry experiment, the instrument will first acquire a survey or precursor scan, referred to as an MS scan, which measures all intact peptide ions eluting into the mass spectrometer at that given time
Summary
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. In a tandem mass spectrometry experiment, the instrument will first acquire a survey or precursor scan, referred to as an MS scan, which measures all intact peptide ions eluting into the mass spectrometer at that given time. A 1994 paper by Mann and Wilm introduced the strategy of searching protein sequence databases using peptide sequence tags interpreted from MS/MS spectra [1] These tags of 3 to 5 consecutive amino acids were inferred by recognizing chains of amino acid mass differences between peaks. In recent years, automated systems for inferring sequence tags have been joined by new tools to Molecular & Cellular Proteomics 10.11
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