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.

Variant values can also be calculated :

• Spectra sum weighting : divide all spectral count values by the number of spectra in the context
• Protein mass weighting : divide all 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.

1. Select the context of your choice (for which protein grouping have been executed)
2. Right-click and select Algorithms > Compute Spectral Count
3. Spectral count results are available in Protein Group