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--- how_to:studio:viewprotset [2016/02/08 13:49]
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 MSQueries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices ======
+====== Display MS Queries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices ======
@@ Line 66: / Line 66: @@
 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|}}
+**View 1** : All the matrices. Each matrix correspond of a cluster composed of linked Proteins/Peptides.
+**View 2** : The currently selected matrix.
+In the example, you can see that PIL1_YEAST and LSP1_YEAST share only one peptide.

Proline

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