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--- how_to:studio:viewprotset [2014/06/20 15:57]
132.168.72.206
+++ how_to:studio:viewprotset [2016/11/10 15:17] (current)
130.79.67.200 [PTM Protein Sites Window]
@@ Line 1: / Line 1: @@
-====== Display PSM, Peptides or Protein Sets of an Identification Summary ======
+====== Display MS Queries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices ======
-===== Functionnality Access =====
+===== Functionality Access =====
 To display data of an Identification Summary:
@@ Line 8: / Line 8: @@
 - right click on an Identification Summary
-- click on the menu "Identification Summary >" and on the sub-menu "PSM", "Peptides" or "Protein Sets"
+- click on the menu "Display Identification Summary >" and on the sub-menu "MSQueries", "PSM", "Peptides", "Protein Sets", "PTM Protein Sites" or "Adjacency Matrices"
-{{:how_to:studio:displayidspopupv3.png|}}
+{{:how_to:studio:popupdisplayidentification.png|}}
+===== MSQueries Window =====
+If you click on MSQueries sub-menu, you obtain this window:
+{{:how_to:studio:msqueryrsm.png|}}
+Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]]
@@ Line 19: / Line 29: @@
 {{:how_to:studio:displayidspsmdialogv3.png|}}
-Note : Abbreviations used are listed [[how_to:studio:abbreviations|here]]
+Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]]
 ===== Peptides Window =====
@@ Line 28: / Line 38: @@
-Upper View : list of all Peptides
+**Upper View**: list of all Peptides
-Middle View : list of all Protein Sets containing the selected peptide.
+**Middle View**: list of all Protein Sets containing the selected peptide.
-Bottom Left View : list of all Proteins of the selected Protein Set
+**Bottom Left View**: list of all Proteins of the selected Protein Set
-Bottom Right View : list of all Peptides of the selected Protein
+**Bottom Right View**: list of all Peptides of the selected Protein
-Note : Abbreviations used are listed [[how_to:studio:abbreviations|here]]
+Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]]
 ===== Protein Sets Window =====
@@ Line 45: / Line 55: @@
-View 1 (at the top) : list of all Protein Sets
+**View 1** (at the top): list of all Protein Sets
+Note : In the column Proteins, 8 (2, 6) means that there are 8 proteins in the Protein Set. 2 in the sameset, 6 in the subset.
+**View 2**: list of all Proteins of the selected Protein Set.
+**View 3**: list of all Peptides of the selected Protein
+**View 4**: Protein Sequence of the previously selected Protein and Spectrum of the selected Peptide.
+Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]]
+===== PTM Protein Sites Window =====
+If you click on PTM Protein Sites sub-menu, you obtain this window:
+{{:how_to:studio:ptmproteinsitewindow.png|}}
+**View 1** (at the top): This view lists all Peptides/PTM. If a peptide contains multiple PTMs, it is displayed multiple times.
+The user can click on "Hide Redundant Peptides" to hide the miss cleavage peptides with the same PTMs.
+The non-redundant modifications are counted and displayed for each type of peptide.
+The user can filter on PTM Modification.
+In the following example, the user keeps only Oxidation on residue M. It is possible to specify no residue, to accept all, or to specify a list of residues.
+{{:how_to:studio:ptmmodificationfilter.png|}}
+**View 2**  : All peptides of the selected Protein
+**View 3**  : Protein Sequence and selected peptide
+===== Adjacency Matrix Window =====
+If you click on Adjacency Matrix sub-menu, you obtain this window:
+{{:how_to:studio:adjacencymatrixwindow.png|}}
-Note : In the column Proteins, 4 (4,0) means that there are 4 proteins in the Protein Set. 4 in the sameset, 0 in the subset.
+**View 1** : All the matrices. Each matrix correspond of a cluster composed of linked Proteins/Peptides.
-View 2 : list of all Proteins of the selected Protein Set.
+**View 2** : The currently selected matrix.
-View 3 : list of all Peptides of the selected Protein
+In the example, you can see that PIL1_YEAST and LSP1_YEAST share only one peptide.
-View 4 : Protein Sequence of the previously selected Protein and Spectrum of the selected Peptide.
-Note : Abbreviations used are listed [[how_to:studio:abbreviations|here]]

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