Skyline does not have an easy way to export the modification sites like that.
There is an Issue open on this which I am supposed to implement a fix for:
https://skyline.ms/issues/home/issues/details.view?issueId=247

Can you tell me what sort of output you'd like to see?
In the Document Grid, I imagine each Protein row would have a "Modified Sites" column which would be a comma separated list of amino acid codes and position in the amino acid. Or, maybe we should have a column at the Peptide level which shows the modifications for that peptide.

If you want to see which amino acids are modified in a peptide, there is a column called "Peptide Modified Sequence" which will show the peptide sequence with modifications in square brackets (e.g. "PEPTIDEC[+57]K") but there's nothing that makes it easy to find out which positions in the protein are modified.

It would be helpful if you could send me a Skyline document with a lot of examples of peptides and proteins where you would like to see this value. It's always helpful to be looking at a user's real world data when we are designing a feature like this.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms and spectral libraries.

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

-- Nick

Dear Nick,
I am pleased for receving your respond. But the problem may not be solved according to your guide. In document grid, "modified site" can not be found, but only show the begin and end position. If the peptide report can exist the colum including the "modified site" in protein, just like the protein "A2A4P0“ in 83 amino acid "S" with phosphorylation, and then we can export the column with S83 means modification happened. Can this problem can be solved?
Best wishes

Hi Nick,

Although the modifications are completely different here you could find a few skyline documents with lots of modified peptides:

https://panoramaweb.org/ULeipzig_ARP_Protein_Carbonylation_Method.url

I would love to see this feature implemented in Skyline! For the moment I had to write a dirty, but functional script that could do the job for peptides that had one modification (excluding Cys carbamidomethyl and Carbamylation).

Things I had to considered while annotating the sites:
- How Skyline counts the aminoacid positions. I think it counts the first aminoacid as 0, right?
- Although I disagree with it, I have seen some people prefer seeing the modification site with respect to the "mature" protein sequence. Some nice annotation summaries can be found in NextProt, but I suppose is very user dependent...
- Towards which proteoform should the mod site be reported? Assuming the peptide is not unique and multiple proteoforms have been imported in the document, could the mod site be reported individually? Even after removing "repeated peptides"?

Thanks!
JC