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.