Patent ID: 7765068

Claim:
A method of determining the structure and origin of a sample protein fragment, comprising: collecting an MS/MS spectrum of the sample protein fragment, identifying the mass of the sample protein fragment, preparing a first set of candidate fragments from the sample protein fragment and a protein sequence selected from a protein sequence database, comprising: selecting a first candidate sequence comprising a terminal amino acid of the protein sequence; generating a further candidate sequence from each candidate sequence, except a last candidate sequence, by: adding a portion of the protein sequence farther away from the terminal amino acid than the candidate sequence, if a mass of the sample protein fragment is equal to or greater than the mass of the candidate sequence within a first tolerance, or deleting a portion of the candidate sequence from an end closest to the terminal amino acid, if the mass of the sample protein fragment is less than the mass of the candidate sequence within a second tolerance including any candidate sequences having a mass which is equal to the mass of the sample protein fragment within a third tolerance, in the first set of candidate fragments; and saving the first set of candidate fragments in a memory; wherein the candidate sequences are subsequences of the protein sequence.