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--- userguide:spectralcount [2010/01/11 09:48]
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+++ userguide:spectralcount [2013/01/28 15:32] (current)
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@@ Line 1: / Line 1: @@
 ====== Spectral count ======
+**See** [[how_to:accessspectralcountdata|how to run spectral count algorithm]]\\
+**See** [[how_to:accessadjustedspectralcountdata|how to run adjusted spectral count algorithm]]\\
 ===== Definition =====
-Spectral count reflects relative abundance of a protein by counting how many times all peptides of a proteins have been fractioned.
-The Spectral Count algorithm can be run for a given context ; it will loop on every protein groups of this context.\\
-FIXME Several other characteristics may be useful to collect.
-===== Run 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.\\
-  - Select the context of your choice (for which protein grouping have been executed)
+Spectral count reflects relative abundance of a protein by counting how many times all peptides of a proteins have been fractioned.
-  - Right-click and select ''Algorithms > Compute Spectral Count''
+  * For Mascot context the spectral count is similar to the number of peptides (which return number of all peptides : similar and duplicate).
-  - Spectral count results are available in Protein Group [[properties]]
+  * 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.
-{{:spectralcountparam.png|Settings spectral count algorithm}}
+===== Adjusted Spectral Count =====
+TODO

hEIDI

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