The Protein Scorer node calculates protein scores and decoy results from different search engines according to the filtered PSMs. During report processing, a peptide filter might exclude peptides and their PSMs from further processing. The Protein Scorer node determines whether the application merges the results from the same search node type when it calculates the protein score. The protein score is the sum of the scores of the individual peptides.

  • For Sequest HT results, the score is the sum of all peptide XCorr values above the specified score threshold. The score threshold is calculated as follows:
  • 0.8 + peptide_charge ´ peptide_relevance_factor
  • where peptide_relevance_factor is an advanced parameter of the Sequest HT node with a default value of 0.4. For each spectrum, only the highest-scoring match is used.
  • For each spectrum and sequence, the application uses only the highest scored peptide. When it performs a search using dynamic modifications, one spectrum might have multiple matches because of permutations of the modification site.
  • The Mascot result score is as follows:
  • - The standard score—The cumulative protein score based on summing the ion scores of the unique peptides identified for that protein. If a peptide was redundantly identified, only the highest-scoring peptide is used.
  • –or–
  • - The MudPIT score—The sum of the “excess of ions” score over the homology or identity threshold for each spectrum plus the average threshold. For MudPIT scoring, the score for each peptide is not its absolute score but the absolute score minus the threshold. Therefore, peptides with a score below the threshold do not contribute to the score. For each peptide, the threshold is the homology threshold, if it exists; otherwise, it is the identity threshold.

By default, the application automatically switches between the standard and the MudPIT score to calculate the protein score in the Mascot node results. It automatically uses the MudPIT score when the number of queries divided by the number of FASTA database entries exceeds 0.001.

The Protein Scorer node has no parameters.