Patent ID: 7783429

Claim:
A method of peptide sequencing from peptide fragment mass data, said method comprising: (a) obtaining peptide fragment mass data, said fragment mass data comprising a plurality of peak data; (b) deriving a plurality of candidate peptide sequences from said peptide fragment mass data; (c) calculating mass spectra for each candidate peptide sequence from said plurality of candidate peptide sequences; and (d) comparing said calculated mass spectra to said peptide fragment mass data for providing at least one identified peptide sequence; wherein the at least one identified peptide sequence is displayed in an output window; wherein said step (b) deriving said plurality of candidate peptide sequences comprises: calculating peptide fragment masses by adding to masses of a proton, hydronium ion, b1 ion and y1 ion masses of one amino acid or more amino acids; searching said plurality of peak data for masses matching said calculated peptide fragment masses to obtain resulting 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 from said 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; 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 identical sequences generated in at least one of the foregoing steps from said potential sequences; wherein the foregoing steps are performed by a computer that is enabled to execute instructions to perform peptide sequencing from mass spectrograph data from a computer-readable media.