Patent ID: 6963807

Claim:
A computer-based method for determining whether or not a first peptide sequence database contains one or more peptide sequences that correspond to an experimental peptide, the method comprising: (a) analyzing a first fragmentation spectrum obtained by mass spectrometry of the experimental peptide to generate a first peak list comprising an assigned mass value for each of a plurality of peaks detected in the first fragmentation spectrum; (b) interpreting the first peak list by a computer-mediated spectral read to construct one or more search sequences (X) and deriving from a fragmentation mass spectrum of the experimental peptide alone or in combination with a primary mass spectrum of the experimental peptide two or more mass data selected from the group consisting of: a mass (M1) of a sequence flanking the N-terminus of X, a mass (M2) of a sequence flanking the C-terminus of X, and a total mass, wherein each search sequence and associated mass data together constitute a search string; (c) searching the first database with at least one search string to determine whether the first database contains one or more candidate sequences that include a search sequence (X) of a search string and any two or more mass data selected from the group consisting of M1, M2 and the total mass associated with that search string; and (d) performing a computer-mediated back-read that tests the candidate sequences, if any, against the first peak list derived from a fragmentation spectrum of the experimental peptide and determining whether one or more candidate sequences match the search sequence (X) of the search string and any two or more mass data selected from the group consisting of M1, M2 and the total mass associated with the search string; where upon, the one or more candidate sequences, if any, that match are identified as corresponding sequences.