AN APPROACH TO CORRELATE TANDEM MASS-SPECTRAL DATA OF PEPTIDES WITH AMINO-ACID-SEQUENCES IN A PROTEIN DATABASE

A method to correlate the uninterpreted tandem mass spectra of peptide s produced under low energy (10-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this me thod the protein database is searched to identify linear amino acid se quences within a mass tolerance of +/- 1u of the precursor ion molecul ar weight. A cross-correlation function is then used to provide a meas urement of similarity between the mass-to-charge ratios for the fragme nt ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. In genera l, a difference greater than 0.1 between the normalized cross-correlat ion functions of the first- and second-ranked search results indicates a successful match between sequence and spectrum. Searches of species -specific protein databases with tandem mass spectra acquired from pep tides obtained from the enzymatically digested total proteins of E. co li and S. cerevisiae cells allowed matching of the spectra to amino ac id sequences within proteins of these organisms. The approach describe d in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.