• The peptide spectral count consist in counting the number of spectra which allow the peptide identification. The number of pepitde spectrum matches.
• Protein basic spectral count (BSC) is the sum of the peptide spectral count for all peptide which identify the protein
• Protein specific spectral count (SSC) is the sum of the peptide spectral count for specific peptide which identify the protein. A specific peptide, is a peptide which does not identify an other protein (or more precisely protein set) in the context of the identification result.
• Protein weigthed spectral count (WSC) is the Protein specific spectral count + weighting based spectral count of shared peptide.

The peptide specificity and the spectral count weight could be defined in the context of the Identification Result where the spectral count is calculated as shown in previous schema, but it can also be done at the parent Identification Result level.

Actually, spectral count is calculated for a set of hierarchy related Identification Results. In other word, this means that Identification Results should have a common parent Identification Results.

Firstly, the peptide spectral count is calculated for each child Identification Results peptide. peptide spectral count =

• Peptide Spectrum Matches Count if Identification Result is a leaf (not issued from a merge)
• Sum of child peptide spectral count in case of identification resulr merge
• Sum of validated child peptide spectral count in case of Search Result merge. Validated child PSMs are PSMs of child Search Result which satisfy validation applied to parent Identification Results.

Once, peptide spectral count is known for each peptide, protein spectral count is calculated using followig rules

• Protein BSC = sum of peptide spectral count
• Protein SSC = sum of peptide spectral count for specific peptide only
• Protein WSC = SSC + weighted peptide spectral count for shared peptides. The weight of a peptide for a given protein (P1) = peptide SC x ( number of specific peptides of P1 /number of peptides specific peptides of all protein identified by the peptide)