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.

Thanks
-Doug