prolineconcepts:spectralcountdef
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prolineconcepts:spectralcountdef [2016/03/24 09:45] 132.168.72.225 [In Proline] |
prolineconcepts:spectralcountdef [2016/07/07 15:18] (current) 132.168.72.225 [In Proline] |
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| ===== Definition ===== | ===== Definition ===== | ||
| - | * The ''peptide spectral count'' consist in counting the number of spectra which matches the current peptide. Thus, it's equal to the number of pepitde spectrum matches (PSM). | + | * The ''peptide spectral count'' consist in counting the number of spectra which matches the current peptide. Thus, it's equal to the number of peptide spectrum matches (PSM). |
| * ''Protein basic spectral count'' (BSC) is equal to the sum of the ''peptide spectral count'' for all peptides which identify the protein. | * ''Protein basic spectral count'' (BSC) is equal to the sum of the ''peptide spectral count'' for all peptides which identify the protein. | ||
| - | * ''Protein specific spectral count'' (SSC) is equal to the sum of the ''peptide spectral count'' for specific peptide only. A specific peptide, is a peptide which does not identify any other protein (or more precisely protein in other protein sets) in the context of the identification summaries . | + | * ''Protein specific spectral count'' (SSC) is equal to the sum of the ''peptide spectral count'' for specific peptide only. A specific peptide, is a peptide which does not identify any other protein (or more precisely protein in other protein sets) in the context of the identification summaries. |
| - | * ''Protein weighted spectral count'' (WSC) is the ''Protein specific spectral count'' + sharing-weigthed spectral count of shared peptide. | + | * ''Protein weighted spectral count'' (WSC) is the ''Protein specific spectral count'' + sharing-weighted spectral count of shared peptide. |
| |{{ :prolineconcepts:scdef.png?500 |}}| | |{{ :prolineconcepts:scdef.png?500 |}}| | ||
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| |P3 | P3 | 4 | 1| 3.25| P3 | 7| 5| 6.5 | | |P3 | P3 | 4 | 1| 3.25| P3 | 7| 5| 6.5 | | ||
| - | __NOTE:__ : | + | __NOTE__: |
| - | In case of multiple level hierarchy (Sample -> Condition1 vs Condition2 -> 3 replicats by conditons), it could make sense to calculate the spectral count weight at "Condition1" and "Condition2" levels rather than "Sample" level to keep the difference involved by the experiment condition. | + | In case of multiple level hierarchy (Sample -> Condition1 vs Condition2 -> 3 replicates by conditions), it could make sense to calculate the spectral count weight at "Condition1" and "Condition2" levels rather than "Sample" level to keep the difference involved by the experiment condition. |
| ===== In Proline ===== | ===== In Proline ===== | ||
| - | Actually, spectral count is calculated for a set of hierarchy related ''Identification Summaries''. In other words, this means that ''Identification Summaries'' should have a common parent. The list of protein to compare or to considere is created at the parent level as the peptide specificity. User can select the dataset where the shared peptides spectral count weight will be calculated. (see previous chapter) | + | Actually, spectral count is calculated for a set of hierarchy related ''Identification Summaries''. In other words, this means that ''Identification Summaries'' should have a common parent. The list of protein to compare or to consider is created at the parent level as the peptide specificity. User can select the dataset where the shared peptides spectral count weight will be calculated. (See previous chapter) |
| Firstly, the ''peptide spectral count'' is calculated using following rules | Firstly, the ''peptide spectral count'' is calculated using following rules | ||
prolineconcepts/spectralcountdef.1458809118.txt.gz · Last modified: 2016/03/24 09:45 by 132.168.72.225
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