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”

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

Note: Abbreviations used are listed here

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

Note: Abbreviations used are listed here

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

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 here

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

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 here

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

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. I it possible to specify no residue to accept all, or to specify a list of residues.

View 2 : All peptides of the selected Protein

View 3 : Protein Sequence and selected peptide

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

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.