Hi Zimeng,
I am just a user like yourself and maybe the developer team has another solution for you. However, this is how I would do it:
- Go to View -> Live Reports -> Document Grid
- Select the "Peptides" default report in the top-left drop-down menu
Here you will see a report with all peptides in your document. You could apply a filter on the Peptide Modified Sequence using the short format of the mass shift of your PTM if it is specific enough to distinguish them from all others. Alternatively you can create a custom Peptides report where the "Peptide Modified Sequence" is reported in alternative ways that might provide more specificity (see attached screenshot).
Once you find that works, apply the filter to show only those that do not have the PTM of interest, select them all and click on the "X" in the document grid to delete them. Then you should be left only with the peptides carrying the PTM of interest from which you can create your targeted PRM list.
I hope this helps!
Sincerely,
Juan C.
DocumentGrid_example.PNG