Shotgun proteomics overview. The proteins of a complex mixture are cut by sequence-specific proteolysis into peptides that are, in turn, fractionated by liquid chromatography. Each peptide is isolated in the mass spectrometer and characterized by MS/MS. A spectrum represents the peptide's pattern of fragmentation, which allows the assignment of an amino acid sequence, including PTM information. The proteins can then be inferred. Quantitation can be also achieved by the shotgun approach for measuring the relative abundance between peptides identified in two distinct samples treated with different labeling methods [1,2].
Cerqueira et al. BMC Genomics 2012 13(Suppl 5):S4 doi:10.1186/1471-2164-13-S5-S4