Fitting cross-linked peptides to an iRT scale

Fitting cross-linked peptides to an iRT scale Juan C. Rojas E.  2023-01-16 05:06

Hi team,

I am trying to fit some cross-linked peptides to an iRT scale (i.e. calculator) generated from endogenous peptides. Unfortunately the column had to be changed, resulting in different retention times. However, I am trying to compensate for this using the background proteome to define some iRTs.

Skyline allows me to add the peptides within the "Edit iRT Calculator" by clicking "Add Results..." but when I try to click OK I am getting a error message (attached).

You will know best, but to me it seems is that here Skyline is not recognizing cross-link modifications?

Any suggestions for a workaround or is it something that has to be patched?

As always, thanks for your time and help.
Juan C.

Nick Shulman responded:  2023-01-16 07:53
Yes, it definitely looks like a bug that Skyline is not allowing crosslinked peptide sequences to be entered in the Edit iRT Calculator dialog. I will try to fix it.

It would be helpful if you could send us your Skyline document.
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:

-- Nick
Nick Shulman responded:  2023-01-31 10:49

Thank you for sending those files over email two weeks ago.
This bug will be fixed in the next update of Skyline-daily and you will be able to use the "Use Results" button etc. to add crosslinked peptides in the Edit iRT Calculator dialog.
-- Nick