Mass spectrometry-based proteolytic mapping for rapid virus identification.

A novel method is proposed for rapid identification of viruses and other organisms that show a low number of biomarkers, based on the construction of databases of organism-specific tryptic peptide masses. The peptide products of any protease that cuts at specific residues can be accommodated. Experimentally, a sample of intact virus, e.g., one collected from the atmosphere, is digested with a selective protease for a short time, and the digestion products are analyzed by MALDI-TOF mass spectrometry without fractionation or purification. In the present proof of concept, the Sindbis virus AR 339 was identified by using the masses of observed tryptic peptide products to query a database composed of tryptic peptide masses generated in silico for six viruses whose genomes have been sequenced. Two algorithms were tested for identification--a direct score-ranking algorithm and an algorithm that evaluates the probability of random matching. The Sindbis virus was unambiguously identified by either approach. The influence of factors such as experimental mass accuracy, number of missed cleavages, and database size on the identification algorithms has also been evaluated, with the objective of extending the approach to other microorganisms.