Protein sequence analysis
   • Problem
    Complete protein sequence coverage
    o antibody confirmation
    o biomarker discovery
    Database search software along is insufficient
                          Protein sequence analysis
      • Possible reasons for incomplete coverage
          •  “non-database” peptides
              o unexpected modifications
              o mutated residues
              o novel peptide
          • database errors
      •   Meanwhile
          Large amount of high-quality spectra are not matched.
     Proposed workflow for in-depth analysis
  • A workflow to identify both the database and 
   “non-database” peptides
  • Objective
   • Maximize protein sequence coverage
   • Explain more high-quality MS/MS spectra
                Proposed workflow for in-depth analysis
      •   Workflow
                                         •
                                            Multiple protein digests with 
           Multiple enzyme               different enzymes
                                         •
                                            High accuracy MS for both 
                                         precursor and fragment ions
            Proposed workflow for in-depth analysis
     • Workflow
        Multiple enzyme
                              •  Identify de novo sequence tags
                              •  Reveal a set of high quality spectra 
     PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. 
     Rapid Commun Mass Spectrom. 2003;17(20):2337-42.