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--- how_to:studio:importmascot [2014/06/20 09:45]
132.168.72.206
+++ how_to:studio:importmascot [2015/10/28 15:04] (current)
132.168.72.237 [Import directly in a Dataset]
@@ Line 23: / Line 23: @@
 - select the file(s) you want to import thanks to the file button (the Parser will be automatically selected according to the type of file selected)
-- select the different parameters
+- select the different parameters (see description below)
 - click on OK button
-**Note 1** : You can only browse the files accessible from the server according to the configuration done by your IT Administrator. Ask him if your files are not reachable. ( look for Setting up Mount-points  in [[setupguide:start|]] page )
+**Note 1** : You can only browse the files accessible from the server according to the configuration done by your IT Administrator. Ask him if your files are not reachable. ( look for //Setting up Mount-points// paragraph in [[setupguide:start|]] page )
+**Note 2** : The **"Save Spectrum Matches"** option does no longer exists. The Spectrum matches can be generated on demand when the Search Result is imported.
+**Note 3** : Proline is able to import OMSSA files compressed with BZip2.
+**__Parameters description__ :**
+  * Software Engine: the software which generated your interrogation file
+  * Instrument: mass-spectrometer used for sample analysis
+  * Peaklist Software: the software used for the peaklist creation
+  * Decoy Strategy: The type of decoy search which was performed.
+    * "No Decoy Database": if the search was performed against a target database only.
+    * "Concatenated Decoy Database": if target and decoy sequences were merged into a single database.
+    * "Software Decoy": if the "Decoy" sequences were generated on-the-fly by your search engine.
+    * Protein Match Decoy Rule: for concatenated searches only. Select the rule to apply for the discrimination of target and decoy protein matches.
+  * Parser Parameters: according to your Software Engine, this will display some extra-parameters.
+    * Mascot:
+      * Ion Score Cutoff: peptide matches with a score lower than this value won't be imported
+      * Subset Threshold: the percentage of score between a given protein match and the master protein match (superset). Protein matches with a relative score lower than <code>Master_protein_score * (1-subset threshold)</code> won't be imported.
+      * Mascot Server URL : URL of the local Mascot server from where some information would be retrieve.
+    * Omssa:
+      * User mod file: TODO
+      * PTM Composition File: TODO
-**Note 2** : Select the **"Save Spectrum Matches"** is important if you want to display annotated spectrums and fragmentation tables. But it takes more time to achieve the import.
 {{:how_to:studio:importidentificationdialogV3.png|}}
@@ Line 51: / Line 75: @@
 ===== Import directly in a Dataset =====
-It is possible to import a Search Result directly in an Dataset. In this case, the Search Result is avaible in "All Imported" too.
+It is possible to import a Search Result directly in a Dataset. In this case, the Search Result is available in "All Imported" too.
+To import a Search Result in a Dataset, right click on a dataset and then click on "Import Search Result..." menu.
-To import a Search Result in a Dataset, right click on a dataset and then click on "Add > Search Result..." menu.
-{{:how_to:studio:importidentificationinaggregatev2.png|}}
+{{:how_to:studio:importsearchresultpopup.png|}}

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