Peptide sequencing from peptide fragmentation mass spectra

Abstract

The invention relates to a method of peptide sequencing from peptide fragment mass data, wherein a step of deriving a plurality of candidate peptide sequences comprises the following steps: calculating peptide fragment masses by adding to masses of a proton, hydronium ion, b1 ion or y1 ion masses of one amino acid or more amino acids; searching a plurality of peak data for masses matching said calculated peptide fragment masses; annotating in all permutations said peak data with amino acid sequences that correspond to said calculated peptide fragment masses, thereby creating one or more potential sequences; extending said potential sequences to resulting masses with additional matching masses by stepwise adding masses of one or more amino acids and searching for masses in said plurality of peak data that match said resulting masses; extending said stepwise additions until said resulting masses correspond to parental peptide masses or said parental peptide masses minus the mass of water, depending on whether the b or y ion series sequences are calculated; and providing at least one identified peptide sequence by deleting sequences from said potential sequences that can not be extended to endpoints of said parental peptide masses, and deleting from said potential sequences identical sequences generated in at least one of the foregoing steps.

Dependencies are inferred from the claim text.