Peptide mass fingerprinting

Peptide mass fingerprinting (PMF) (also known as protein fingerprinting) is an analytical technique for protein identification that was developed 1993 by several groups independently. These masses are then in silico compared to either a database containing known protein sequences or even the genome. Computer programs translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides with the same protease (for example trypsin), and calculate the absolute masses of the peptides from each protein. They then compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match. The great advantage is that only the masses of the peptides have to be known (so de novo sequencing is not necessary). A disadvantage is that the protein sequence has to be present in the database of interest. Additionally most PMF algorithms assume the peptides come from a single protein.

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