====== Spectral count ======

**See** [[how_to:accessspectralcountdata|how to run spectral count algorithm]]\\
**See** [[how_to:accessadjustedspectralcountdata|how to run adjusted spectral count algorithm]]\\

===== Definition =====


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 

  
FIXME Several other characteristics may be useful to collect.

===== Adjusted Spectral Count =====

TODO