See how to run spectral count algorithm
See how to run adjusted spectral count algorithm

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.

TODO