Isotope prediction issue upon data import

Isotope prediction issue upon data import dbc007  2023-12-07 13:10

Hello --

When a new document is started (i.e. - set molecule/trans settings, transition list imported via copy/paste from spreadsheet, raw data imported as Agilent .D files or Thermo .RAW files) the isotope prediction algorithm does not include the isotopologue of highest abundance (what we might think of as the “main” monoisotopic signal for each imported compound). To be clear, these are high-res MS1 data. Therefore the idotp does not get calculated correctly. I can fix this by simply saving, closing, and re-opening the Skyline file, which isn’t such a big deal, but this happens every time I start a new skyline file. Happens to others in my lab also across different computers, and it's been happening across version releases. I think it occurred in version 22, continues in the latest v23 release, and also in the most recent Skyline Daily release (attempted and replicated issue on 7 Dec 2023).

I have attached a PPT file with screenshots and some more description of what we see. As mentioned, if I close the file and re-open it, the issue is gone forever (in that file, but comes back when we make a new one). There is some (rather ugly) data shown in the file, but it illustrates my specific problem.

Has anyone else seen this issue? If it was a one-off bug I would have just thought nothing of it, but it's been happening routinely for at least a few months.


Nick Shulman responded:  2023-12-07 13:24
I believe another user has reported this issue:

We are working on a fix for this:

The code that has the bug in it is a little complicated, so I have not actually managed to commit the fix to the Skyline code base.

It might be helpful if you could send us your Skyline document and the transition list that you were trying to insert.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries

If that .zip file and/or your transition list are less than 50MB you can attach them to this support request.
You can upload larger files here:

It would be really helpful if you could give us permission to use your data files when we write an automated test for Skyline to ensure that this bug remains fixed. That data would become a permanent part of the Skyline open source project, so, if there is anything confidential or copyrighted in your data then we cannot use it.

(It's also possible that the bug you are running into is different than the one reported by this other user, which we will be able to figure out after we see your data files).
-- Nick