how_to:studio:viewprotset
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how_to:studio:viewprotset [2016/02/08 13:48] 132.168.72.206 |
how_to:studio:viewprotset [2016/11/10 15:17] (current) 130.79.67.200 [PTM Protein Sites Window] |
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| - | ====== Display MSQueries, PSM, Peptides or Protein Sets of an Identification Summary ====== | + | ====== Display MS Queries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices ====== |
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| - right click on an Identification Summary | - right click on an Identification Summary | ||
| - | - click on the menu "Display Identification Summary >" and on the sub-menu "MSQueries", "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:popupdisplayidentification.png|}} | {{:how_to:studio:popupdisplayidentification.png|}} | ||
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| Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]] | Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]] | ||
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| + | ===== PTM Protein Sites Window ===== | ||
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| + | If you click on PTM Protein Sites sub-menu, you obtain this window: | ||
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| + | {{:how_to:studio:ptmproteinsitewindow.png|}} | ||
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| + | **View 1** (at the top): This view lists all Peptides/PTM. If a peptide contains multiple PTMs, it is displayed multiple times. | ||
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| + | 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. | ||
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| + | The user can filter on PTM Modification. | ||
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| + | 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. | ||
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| + | {{:how_to:studio:ptmmodificationfilter.png|}} | ||
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| + | **View 2** : All peptides of the selected Protein | ||
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| + | **View 3** : Protein Sequence and selected peptide | ||
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| + | ===== Adjacency Matrix Window ===== | ||
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| + | If you click on Adjacency Matrix sub-menu, you obtain this window: | ||
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| + | {{:how_to:studio:adjacencymatrixwindow.png|}} | ||
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| + | **View 1** : All the matrices. Each matrix correspond of a cluster composed of linked Proteins/Peptides. | ||
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| + | **View 2** : The currently selected matrix. | ||
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| + | In the example, you can see that PIL1_YEAST and LSP1_YEAST share only one peptide. | ||
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how_to/studio/viewprotset.1454935703.txt.gz · Last modified: 2016/02/08 13:48 by 132.168.72.206
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