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--- userguide:pride_inspector [2011/03/08 14:03]
132.168.74.230
+++ userguide:pride_inspector [2012/03/14 12:06] (current)
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@@ Line 1: / Line 1: @@
 ====== PRIDE Inspector ======
+PRIDE Inspector is an application to visualize and perform a first quality assessment of MS data. \\
+With PRIDE Inspector users can have a close look at their own data before the actual submission, or access data already in PRIDE for data mining purposes.
+===== Download =====
 PRIDE Inspector is available at [[http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector]]\\
@@ Line 5: / Line 11: @@
   * Dowload the pride-inspector-X.Y.Z.zip file, then unzip.\\
   * To execute PRIDE Inspector, double-click on pride-inspector-X.Y.Z.jar\\
+  * To open a PRIDE XML file, select the ''File->Open File...'' menu and browse to an PRIDE XML file
+{{:userguide:prideinspector_1.png|}}
+===== FAQ =====
+==== Why do I not get the same number of peptides between hEIDI & Pride Inspector ? ====
+{{:userguide:pride_peptidecountinprideinspectorandheidi.png|}}
+**Peptide unicity in an hEIDI context is based on sequence & calculated mass.**\\
+For example, the peptide ''FASFIDKVR'' is represented by one peptide node in the ''Peptide View''. \\
+This peptide matches on 15 master proteins (see the ''Protein Group(s) match(es)'' column) but 7 other proteins as well (information not visible in hEIDI)\\
+{{:userguide:pride_onepeptideinheidi.png|}}
+**In Pride Inspector, a row exists for each peptide-protein match.**\\
+For example, the peptide ''FASFIDKVR'' appears 22 times: one row for each protein match.
-PRIDE Inspector is an application to visualize and perform a first quality assessment of MS data. With PRIDE Inspector users can have a close look at their own data before the actual submission, or access data already in PRIDE for data mining purposes.
+{{:userguide:pride_onepeptideinprideinspector.png|}}
+So, the number of peptides in Pride Inspector is generally bigger than the peptide count in a User context.
+===== The Experiment Details tab =====
+{{:userguide:prideinspector_2.png|}}

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