Peptide mass fingerprinting (PMF) is an analytical technique for protein identification. Basically, the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. Then these masses are compared to either a database containing known protein sequences or even the genome sequence which can be translated into proteins through computer programs. Then the absolute masses of the peptides from each protein are calculated theoretically for mass comparison between the peptides of the unknown protein and the theoretical peptide masses of each protein to find the best match.
The advantage of PMF method is that only the masses of the peptides is need to be known, while time-consuming de novo peptide sequencing is then unnecessary, as long as the protein sequence is present in the database of interest. Additionally, most PMF algorithms assume that the peptides come from a single protein while the presence of a mixture can significantly complicate the analysis and potentially compromise the results, thus an isolated protein is needed for the PMF based protein identification. Mixtures exceeding a number of 2-3 proteins typically require the additional use of MS/MS based protein identification to achieve sufficient specificity of identification.
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