When you use the PSM Grouper node in the consensus workflow, the Proteome Discoverer application adds columns of information about modifications to the Peptide Groups page of the result file.
The content of the Modifications column shown in the Peptide Groups page is a merged list of all the modifications found in the PSMs belonging to the peptide group. The following figure shows the format of each kind of modification.
| No. | Description | No. | Description |
|---|---|---|---|
1 | Number of modifications of this type in the peptide | 3 | Target amino acid and position in the peptide |
2 | Type of modification as shown in the Chemical Modifications view | 4 | Site probability, when available |
The PSM Grouper node creates two different modification columns. One column contains all possible modification sites, and the other one contains only the best possible site for each modification.
When a modification has no unique “best” position, the application displays the modification with the target amino acid, but without specifying the best position. In this case, you must review the PSMs of the peptide group by clicking Show Associated Tables on the results pages.
Depending on the setting of the Modification Sites Shown parameter of the node, the application displays one or both of these columns. If one of the columns is hidden, you can display it by using the Field Chooser in the upper left corner of the result page. You can restrict the display of modifications in the Peptide Groups page through the parameter settings of the PSM Grouper node. For information on these parameters, see PSM Grouper node.