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--- userguide:filtres [2010/01/12 14:59]
132.168.73.9
+++ userguide:filtres [2011/12/19 16:32] (current)
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@@ Line 47: / Line 47: @@
 ==== Master Protein Filter ====
 By default the protein groups are represented by a master protein. This master protein is the same as the one defined by mascot.
-If it doesn't suit your needs you have the possibility to change the master proteins one by one in the interface OR, in one step for all the protein group, by using the associated filter.
+If it doesn't suit your needs you have the possibility to change the master proteins one by one in the interface OR, in one step for all the protein groups, by using the associated filter.
-This filter using **rules** to determine which protein in the same set must be set as master. To have sufficient complexity you can **composed** multiple rules together.\\
+This filter use **rules** to determine which protein in the same set must be set as master. To have sufficient complexity you can **composed** multiple rules together.\\
-:!: **In a protein group the FIRST protein matches the composition of rules will be set as master.**
+:!: **In a protein group the FIRST protein which matches the rules composition will be set as master.** \\
-:!: If no protein in the protein group matches the composition of rules, the old one is kept.
+:!: If no protein in the protein group matches the rules composition, the old one is kept. \\
+:!: If the new master don't match some ambiguous peptides (because they belonging only to the old master) they will be deleted without asking (in contrary of manual master protein changing).
 === The rules ===
@@ Line 86: / Line 87: @@
 == Example 2 ==
-{{:userguide:master-filter-window-2.png|}}
+{{:userguide:master-filter-window-2.png|}}\\
 In this example, will be set as master the first protein of each protein group which have :
   * Its Accession number not containing 'P5098'
@@ Line 97: / Line 98: @@
 => You want to set as master only protein belong to HUMAN or MOUSE but never a particular protein which have an accession containing 'P5098'.
+----
+==== FPR Seeker Filter ====
+The False Positive Rate (FPR) Seeker Filter will search for the best filter to reach the given FPR.
+Then launch it with the right parameters.\\
+Nota : 'Best' is defined as the one which can lead to a FPR inferior to the given one while keeping the most forward (if both are equals, ScoreAndRank will be chosen by default)\\
+The FPR is calculated as 2x''Reverse''/(''Reverse''+''Forward''). Where ''Reverse'' is the number of peptide matching on a ''Reverse'' protein and ''Forward'' is the number of peptide matching on a ''Forward'' protein (peptide matching on both type are not counted).\\
+In IRMa you can check the FPR in the [[statistics|statistics window]], into the first tab.
+=== How to use ===
+You can access to the FPR Seeker Filter in the Tools menu => Filters => FPR Seeker\\
+{{:userguide:fprseeker-menu.png}}\\
+The following window will be displayed :\\
+{{:userguide:fprseeker-dialog.png}}
+=== Result ===
+The result FPR can be seen in statistics window :\\
+{{:userguide:statistics-fpr-closeup.png}}\\
+And the chained filter can be verified in Tools => Filters => Filter History:\\
+{{:userguide:fprseeker-result.png}}
+----
+==== Single Match per Query Filter ====
+This filter keep only ONE match per query. The best match is kept; as best is defined as the one with highest score. If there is equality the match leading to the master Protein with highest score will be chosen. If there is still equality the first peptide encountered is arbitrary chosen.\\
+{{:userguide:singlematchwindow.png|}} \\
+=== Example 1 ===
+In this example the query n°20 has 4 matches leading to protein (AGVLAEVR, LNIPTTR, NLLADLR, LDICQLR) (**Fig 1**). As the first (AGVLAEVR) have the higher score (23.15, **Fig 2**) all the others will be mark as ambiguous by the filter.\\
+{{:userguide:singlematchexample2.png|}}
+\\ **Fig 1** \\
+{{:userguide:singlematchexample1.png|}}
+\\ **Fig 2** \\
+=== Example 2 ===
+The query n°1060 has 2 matches leading to proteins (LLIYGA**ST**R & LLIYGA**TS**R). Due to T & S swapping the two matches has the same score (35.14). As the second one (LLIYGA**TS**R) leads to a protein with the higher score (212 opposed to 127) the first one will be mark as ambiguous.
+\\
+{{:userguide:singlematchexample3.png|}}\\
+**Nota** : in that example, apply the Score & Rank filter with parameters to only kept rank 1 peptides would have lead to mark the second one as ambiguous, in contrary of the Single Match per Query Filter

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