The Spectral Count algorithm can be run for a given context and will loop on every protein groups of this context to calculate this property.
Spectral count reflects relative abundance of a protein by counting how many times all peptides of a proteins have been fractioned.
For Mascot context the spectral count is similar to the number of peptides (which return number of all peptides : similar and duplicate).
For user context, this algorithm will count how many leaf peptides have been grouped for each peptide of the protein group, thus spectral count and number of peptides are different.
A another spectral count value, Proteotypique Spectral Count, calculate the number of proteotypic peptide for each protein (typical protein). Proteotypic peptides are peptides which match only proteins of a single protein group.
Variant values can also be calculated :
Spectra sum weighting : divide all spectral count (total spectral count) values by the number of spectra in the context
Protein mass weighting : divide all spectral count(total spectral count) values by each master protein mass; A Scale factor can be applied to all Protein mass weighting spectral count values
Several other characteristics may be useful to collect.
Adjusted Spectral Count