Protein identification: Identification of a protein classically requires complete or partial protein sequence. A partial sequence can allow protein identification by comparing it with the sequences of the proteins available in protein sequence databases. A protein can therefore be identified by doing sequencing using MS. However, it may not be required to determine the sequence of a protein for its identification. A typical scheme for protein identification is shown in Figure 13.5.

Figure 13.5 Protein identification using mass spectrometry

A protein is cleaved into smaller peptide fragments using a sequence specific enzyme, usually trypsin or chymotrypsin. Trypsin cleaves at the C-terminal side of lysine and arginine residues while chymotrypsin cleaves at the C-terminal side of aromatic amino acids, phenylalanine, tyrosine, and tryptophan. The masses of these fragments are then searched in peptide mass databases. This method is termed as the peptide mass fingerprinting. If no match is found in the databases, the peptides are sequenced using another MS as discussed earlier; the protein is identified by searching the sequences of the fragments in the protein sequences databases. Protein identification using MS is central to the proteomic studies. A typical proteomic analysis is briefly summarized in Figure 13.6

Figure 13.6 Outline of a proteomics experiment