Hi Zhen Long,
The Skyline Peptide Settings - Modifications tab is so flexible that you should be able to define just about any modification you can think of. People have even used them to fake Skyline into measuring lipids defined as 2 amino acid sequences with "modifications" on them.

https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00841

And also for measuring cross-linked peptide sequences where the linked peptide was defined as a modification.

The pre-defined modifications in Skyline that you can just choose by name come from Unimod:

http://www.unimod.org

So, if you want to see a named modification that is missing from Skyline, the best way to get that would be to get it added to Unimod with an official name. We are a little behind having last updated a few years ago. If you feel your modifications are already there, please point us to the Unimod ID you wish to have added.

Otherwise, you are free to define any modification you like, ideally by giving Skyline its amino acid specificity and a chemical formula, but you can also define modification just by delta mass, as you have in your support request.

There is a webinar on working with modifications in Skyline that may help:

https://skyline.ms/webinar10.url

Good luck defining these custom modifications, or again, if you see them defined in Unimod, please just point us to them. Thanks for using Skyline in your research.

--Brendan