There is no way to do this right now, but I am supposed to implement this feature.
I do hope to have something working in a few weeks.

It would be very helpful if you could send me your Skyline document so I could see another example of how someone might want to use this upcoming feature.
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.

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

Thank you very much for your reply. I uploaded my Skyline document following your link.

I work in the French metabolomics and fluxomics infrastructure called MetaboHUB and we have decided to use Skyline for much of our data processing. I've already contacted you about some problems specific to metabolomics.
After discussion with my colleagues, we think it would be very interesting to discuss with you (in a meeting) how we can use Skyline for all our targeted processing. And potentially the bricks we're missing.
Please let me know if you are interested.
Yours sincerely
Maud

Hello Maud,

Yes, we'd be very interested to know where Skyline might be improved to suit your workflow. Let's arrange a meeting to find out what your priorities might be. My schedule is generally quite flexible, so just propose something and it will probably be fine. You can email me at bspratt @ proteinms.net

Best regards,

Brian Pratt

Maud,

Thank you for sending that dataset.
I am working on this feature now, and you can see some screenshots here:
https://github.com/ProteoWizard/pwiz/pull/2797

Attached is a screenshot of how the calibration curve for your "2PG_3PG C13" molecule might look.
I have designated that the "Surrogate External Standard" molecule is "2PG_3PG", and so, the "Unknown" points in the graph come from "2PG_3PG C13" and the "Standard" points come from "2PG_3PG".

Let me know whether this looks like a good way to implement things.
-- Nick

thanks a lot it's perfect. when do you plan to release this new version?
have a nice day,
Maud

This feature will be available in the next Skyline-daily which will probably be released in about a week.
If you would like to use this feature before then, you can install the following special Skyline-daily build:
https://proteome.gs.washington.edu/~nicksh/SkylineDailyPreview/
The special Skyline-daily installer has not been cryptographically signed so Windows might warn you against installing it, so you might have to hunt around for the "Run anyway" button. The special Skyline-daily will appear on the Windows Start Menu as "Skyline preview".
-- Nick