I am not sure I understand your question.

Skyline has a lot of support for post translational modifications.
This is the webinar that I point people at when they have questions about modifications in Skyline:
https://skyline.ms/Webinar10.url

If you want to extract chromatograms for the peptide that remains after the sodium ion falls off the peptide, then you should define some "Losses" for the modification.
If you want to extract chromatograms for the ion that is no longer attached to the peptide then you should go to the "Filter" tab at "Settings > Transition Settings" and add some "Custom product ions" to the "Special ions" list.

The only sort of ionization that Skyline supports for peptides is protonation.
If you want to work with some other sort of ionization, then you will need to pretend that your peptides are actually small molecules, and you will need to provide the chemical formula for all of the precursor and product ions.
The following columns in the Document Grid may be helpful for figuring out the chemical formula of the precursor and product ions:
Molecule Formula
Precursor Ion Formula
Precursor Neutral Formula
Product Ion Formula
Product Neutral Formula

You can learn more about the Document Grid here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick

Thanks for your reply.

I'll try to rephrase the question. I'm running an LCMS method on a BSA protein digest. The peptides I'm seeing are from precursors that have Na and K adducts. For example, on a 2+ precursor, I see the [M+2H], [M+H+Na], and [M+H+K] adducts. I'm trying to find a way for Skyline to extract the precursor with these various protonation/adducts states.

But I think you answered my question. I'll have to use the Small molecule (or Mixed?) interface and manually put in the various adducts to then have Skyline extract those.

Thanks,
Josh

One thing that might actually work for you would be to tell Skyline that you have an isotope modification whose chemical formula is "Na-H".
That is, it's an isotope modification which replaces a hydrogen with a sodium.
Skyline expects that isotope modifications will have the same retention time as the unlabeled peptide, so it's likely that this will result in the behavior that you want.
One problem with this technique is that you have to apply it to a particular amino acid. If you apply this isotope modification to the C-terminal of the peptide then all of the y ions will have the sodium atom attached which may or may not be what you want.
-- Nick

This is perfect, thanks. I don't track very many b-ions, so I can just place it at the N-terminus.

It's worth noting that Skyline only supports protonation for peptides because that's the only model we have for fragmentation. Other adducts, I'm told, will lead to other fragmentation patterns. So, proceed with caution. You might do better with the small molecule approach and explicitly stating the fragments that are anticipated. I don't know how much of a problem this will be in your case but I thought it should be mentioned.

- Brian