Mass Spectrometry for Protein Identification

The starting point is a given protein sample that may be a single protein or a complex mixture of different proteins. An enzyme, often trypsin, is used to digest the proteins to peptides. In most cases, one or more stages of chromatography are applied to regulate the flow of peptides into the mass spectrometer. Peptides are then selected for one at a time in the first stage of mass analysis. Each isolated peptide is induced to fragment by collision in the second stage of mass analysis. The fragments are captured to synthesize a MS/MS spectrum.