====== Display MS Queries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices ======


===== Functionality Access =====

To display data of an Identification Summary:

- right click on an Identification Summary

- 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|}}



===== 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]]


===== PSM  Window =====

If you click on PSM sub-menu, you obtain this window:

{{:how_to:studio:displayidspsmdialogv3.png|}}

Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]]

===== Peptides Window =====

If you click on Peptides sub-menu, you obtain this window:

{{:how_to:studio:displayidspetidesdialogv3.png|}}


**Upper View**: list of all Peptides

**Middle View**: list of all Protein Sets containing the selected peptide.

**Bottom Left View**: list of all Proteins of the selected Protein Set 

**Bottom Right View**: list of all Peptides of the selected Protein

Note: Abbreviations used are listed [[how_to:studio:abbreviations|here]]

===== Protein Sets Window =====

If you click on Protein Sets sub-menu, you obtain this window:

{{:how_to:studio:displayidsproteinsetspopupv3.png|}}


**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|}}

**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.