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

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 peptide matches 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.

Not yet implemented