userguide:spectralcount
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userguide:spectralcount [2010/01/11 10:31] 132.168.73.247 |
userguide:spectralcount [2013/01/28 15:32] (current) 132.168.72.131 |
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| ====== Spectral count ====== | ====== Spectral count ====== | ||
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| + | **See** [[how_to:accessspectralcountdata|how to run spectral count algorithm]]\\ | ||
| + | **See** [[how_to:accessadjustedspectralcountdata|how to run adjusted spectral count algorithm]]\\ | ||
| ===== Definition ===== | ===== Definition ===== | ||
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| 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.\\ | 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.\\ | ||
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| * For Mascot context the spectral count is similar to the number of peptides (which return number of all peptides : similar and duplicate). | * 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. | * 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. | ||
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| + | 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 : | Variant values can also be calculated : | ||
| - | * Spectra sum weighting : divide all spectral count values by the number of spectra in the context | + | * 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 values by each master protein mass; A Scale factor can be applied to all Protein mass weighting spectral count values | + | * 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 |
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| FIXME Several other characteristics may be useful to collect. | FIXME Several other characteristics may be useful to collect. | ||
| - | ===== Run Spectral Count algorithm ===== | + | ===== Adjusted Spectral Count ===== |
| - | - Select the context of your choice (for which protein grouping have been executed) | + | |
| - | - Right-click and select ''Algorithms > Compute Spectral Count'' | + | |
| - | - Spectral count results are available in Protein Group [[properties]] | + | |
| - | + | ||
| - | {{:spectralcountparam.png|Settings spectral count algorithm}} | + | |
| + | TODO | ||
userguide/spectralcount.1263202261.txt.gz · Last modified: 2010/01/11 10:31 by 132.168.73.247
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