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Spectral count


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


userguide/spectralcount.txt · Last modified: 2013/01/28 15:32 by