Patent ID: 7805253

Claim:
A system for identifying proteins and modifications from two or more identification methods, comprising: a mass spectrometer that measures a plurality of spectra from a sample; and a processor in communication with the mass spectrometer that receives the plurality of spectra from the mass spectrometer and produces a plurality of peak lists from the plurality of spectra, performs a first identification method that compares a first peak list from the plurality of peak lists with a peak list generated by computationally digesting a first protein database producing a first list of proteins from the comparison, performs a second identification method that applies a de novo peptide sequencing technique to a second peak list from the plurality of peak lists producing one or more putative sequences and matches the one or more putative sequences to a second protein database using an alignment tool producing a second list of proteins from the matching, if a protein of the second list of proteins matches a protein of the first list of proteins, performs a first comparison of the precursor peptide of the second peak list to a full peptide sequence found in the protein, if the precursor peptide does not match the full peptide sequence in the first comparison, performs a second comparison of a difference between the precursor peptide and the full peptide sequence to a modification database, and if a modification from the modification database that matches the difference is found from the second comparison, identifies the protein in the sample from the precursor peptide and the modification.