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. Author manuscript; available in PMC: 2014 Feb 6.
Published in final edited form as: J Am Chem Soc. 2013 Jan 16;135(5):1629–1640. doi: 10.1021/ja3094313

Figure 1.

Figure 1

Protein sequencing becomes protein identification. In both strategies the intact protein is digested with a protease, typically trypsin which cleaves after arginine or lysine, to produce a collection of peptides. By using liquid separations coupled to a tandem mass spectrometer, peptide ions are fragmented as they elute into the instrument. In protein sequencing the tandem mass spectrum is interpreted to determine the amino acid sequence de novo. In protein identification, the tandem mass spectrum is searched through a collection of protein sequences to find the best amino acid sequence match to the spectrum.