Protein Identification from Tandem Mass Spectra by Database Searching.
Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, able to identify proteins, characterize post-translational modifications, and provide semiquantitative measurements of relative protein abundance. This manuscript describes the concepts, prerequisites, and methods required to analyze a tandem mass spectrometry dataset in order to identify its proteins, by using a tandem mass spectrometry search engine to search protein sequence databases. The discussion includes instructions for extraction, preparation, and formatting of spectral datafiles, selection of appropriate search parameter settings, and basic interpretation of the results.
Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA. nje5@georgetown.edu.
Nathan J
NJ
Edwards
D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D010455:Peptides / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods; D064878:Web Browser
D010455:Peptides; D011506:Proteins
MS/MS spectra; Peptide identification; Protein identification; Protein sequence databases; Search engine