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--- prolineconcepts:rsvalidation [2014/02/04 09:29]
132.168.72.206
+++ prolineconcepts:rsvalidation [2015/07/10 11:05] (current)
132.168.72.225
@@ Line 3: / Line 3: @@
 Once a result file have been imported and a search result created, the validation is performed in 4 mains steps :
-  - [[.:rsvalidation#Peptide Matches Filtering|Peptide Matches filtering]] and [[.:rsvalidation#Peptide Matches Validation|validation]]
   - [[prolineconcepts:PeptideMatchesFilteringAndValidation|Peptide Matches filtering and Validation]]
   - [[.:ProteinInferer|Protein Inference]] (peptides and proteins grouping)
@@ Line 9: / Line 8: @@
   - [[prolineconcepts:ProteinSetsFilteringAndValidation|Protein Sets Filtering and Validation]]
-Finally, the [[.:rs_rsm|Identification Result]] issued from these steps is stored in the identification database. Different validation of a Search Result can be performed and a new Identification Summary of this Search Result is created for each validation.
+Finally, the [[.:rsm|Identification Result]] issued from these steps is stored in the identification database. Different validation of a Search Result can be performed and a new Identification Summary of this Search Result is created for each validation.
-===== Peptide Matches Filtering =====
-Peptide Matches identified in search result can be filtered using one or multiple predefined filters (describes here after). Only validated peptide matches will be considered for further steps.\\
-==== Basic Score Filter ====
-All PSMs which score is lower than a given threshold are invalidated.
-==== Pretty Rank Filter ====
-This filtering is performed after having temporarily joined target and decoy PSMs corresponding to the same query (only really needed for separated forward/reverse database searches). Then for each query, PSMs from target and decoy are sorted by their score. A rank (Mascot pretty rank) is computed for each PSM depending on their score position: PSM with almost equal score (difference < 0.1) are assigned the same rank.
-All PSMs with rank greater than specified one are invalidated.
-==== Minimum Sequence length Filter ====
-PSMs corresponding to short peptide sequences (length lower than the provided one) can be invalidated using this parameter.
-==== Mascot eValue Filter ====
-Allows to filter PSMs by using the Mascot expectation value (e-value) which reflects the difference between the PSM score and the Mascot identity threshold (p=0.05).
-PSMs having an e-value greater than the specified one are invalidated.
-==== Mascot adjusted eValue Filter ====
-Proline is able to compute an adjusted e-value. It first selects the lowest threshold between the identity and homology ones (p=0.05). Then it computes the e-value using this selected threshold.
-PSMs having an adjusted e-value greater than the specified one are invalidated.
-==== Mascot p-value on Identity Filter ====
-Given a specific p-value, the Mascot identity threshold is calculated for each query and all peptide matches associated to the query with a score lower than calculated identity threshold are invalidated.\\
-When parsing Mascot result file, the number of PSM candidate for a spectra is saved and could be used to recalculate identity threshold for any p-value.
-==== Mascot p-value on homology Filter ====
-Given a specific p-value, the Mascot homology threshold is inferred for each query and all peptide matches associated to the query with a score lower than calculated homology threshold are invalidated.
-===== Peptide Matches Validation =====
-Specify an expected FDR and tune a specified filter in order to obtain this FDR.
-See how[[prolineconcepts:fdrestimator| FDR is calculated]]
-Once previously described pre-filters have been applied, a validation algorithm can be run to control the FDR: given a criteria, the system will estimate the better threshold value in order to reach a specific FDR.

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