They are multiple algorithm than could be use to calculate the Proteins and Proteins Sets score. Actually, when

• importing Mascot result file : the standard scoring is used
• importing OMSSA result file : …
• validating an identification : depending on the installation (see your administrator), any of the following algorithm could been set

Each individual protein is scored according to all peptide matches associated with this protein, independently of any validation of these peptide matches.

Each individual protein set is scored according to the peptide matches belonging to this protein set (see inference).

The score associated to each identified protein (or protein set) is the sum of the score of all peptide matches identifying the protein (same set protein). In case of duplicate peptide matches (peptide matched by multiple queries) only the match with the best score is considered.

The score associated to each identified protein (or protein sets) is the sum of the offset between best peptide matches (see below) score and corresponding threshold. Peptide matches considered for a protein (or protein set) is all peptide matches identifying that protein (or a same set protein). In case of duplicate peptide matches (peptide matched by multiple queries) only the best score match is considered.

“corresponding threshold” is homology or identity threshold, at 5% p-value. In case of separated target-decoy searches : If homology is defined in decoy search, use decoy value else use target value. In case of identity, if both target and decoy are defined, use mean of values.

Not yet implemented