Procedure

  1. From the application menu bar, select Administration > Configuration.
  2. Under Processing Settings, expand the Sequest folder.
  3. Select Sequest Protein Score.
  4. The Protein Scoring Options configuration parameter opens. For information on this parameter, see Sequest HT node.
  6. In the Peptide Relevance Factor box of the Protein Scoring Options, specify a factor to apply to the protein score.
  7. The Proteome Discoverer application calculates the protein score for a protein as follows:
    Protein score = (Sum of all cross-correlation factors ≥ 0.8) + (Peptide charge × Peptide relevance factor)protein_score = (sum_of_all_cross-correlation_factors_of_0.8_or_above) + (peptide_charge × peptide_relevance_factor)