prolineconcepts:spectralcountdef
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prolineconcepts:spectralcountdef [2015/07/10 15:26] 132.168.72.225 [Specificity and weight reference] |
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| 2| P3 | 7| 7| 7 | | |P3 | P3 | 4 | 1| 2| P3 | 7| 7| 7 | | ||
| - | Again, when considering specificity at protein set level, the result of spectral count in Replicat2 is not representative, as it has a null SSC and WSC. **This calculation was not retain!** | + | Again, when considering specificity at child level, the result of spectral count in Replicat2 is not representative, as it has a null SSC and WSC. **This calculation was not retain!** |
| A way to make some correction is to define the specificity of the peptide and their weight at the parent level, and apply it at the child level. Therefore, specific peptides for P2 is pe8 and for P3 it is pe6 and pe7. | A way to make some correction is to define the specificity of the peptide and their weight at the parent level, and apply it at the child level. Therefore, specific peptides for P2 is pe8 and for P3 it is pe6 and pe7. | ||
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| |P2 | P2 | 5 | 2| 2.75| P2 | 2| 0| 0.5| | |P2 | P2 | 5 | 2| 2.75| P2 | 2| 0| 0.5| | ||
| |P3 | P3 | 4 | 1| 3.25| P3 | 7| 5| 6.5 | | |P3 | P3 | 4 | 1| 3.25| P3 | 7| 5| 6.5 | | ||
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| + | __NOTE__: | ||
| + | |||
| + | 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 weight for spectral count (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 | ||
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| * Sum of validated child ''peptide spectral count'' in case of Search Result merge. Validated child PSMs are PSMs which satisfy validation applied to parent ''Identification Summaries''. | * Sum of validated child ''peptide spectral count'' in case of Search Result merge. Validated child PSMs are PSMs which satisfy validation applied to parent ''Identification Summaries''. | ||
| - | Once, ''peptide spectral count'' is known for each peptide, protein spectral count is calculated using followig rules | + | Once, ''peptide spectral count'' is known for each peptide, protein spectral count is calculated using following rules |
| * Protein BSC = sum of ''peptide spectral count'' | * Protein BSC = sum of ''peptide spectral count'' | ||
| * Protein SSC = sum of ''peptide spectral count'' for specific peptide only | * Protein SSC = sum of ''peptide spectral count'' for specific peptide only | ||
| - | * Protein WSC = SSC + weighted ''peptide spectral count'' for shared peptides. The weight of a peptide for a given protein (P1) = peptide SC x ( number of specific PSM of P1 /number of specific PSMs of all protein identified by the peptide). See explanation in previous chapter | + | * Protein WSC = SSC + weighted ''peptide spectral count'' for shared peptides. The weight of a peptide for a given protein (P1) = peptide SC x (number of specific PSM of P1 /number of specific PSMs of all protein identified by the peptide). See explanation in previous chapter |
prolineconcepts/spectralcountdef.1436534781.txt.gz · Last modified: 2015/07/10 15:26 by 132.168.72.225
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