New version (V23) can't properly work on the data processing for CE optimization

New version (V23) can't properly work on the data processing for CE optimization hsiaoyc  2024-01-17 04:02

Chromatogram doesn't show multiple transition in "single" transition view, but in "all" transition view.
Adjusting peak boundaries will lose ramping data of peak area.

The former version (V22) was workable, and where should I get the install for the V22. I urgently need to process the CE optimization data.

Nick Shulman responded:  2024-01-17 06:57
You can install older versions of Skyline from the "Unplugged" installer page:
After you click the "I agree" button an "Archive" link will appear which will take you to a page where you can download older versions of Skyline.

Which type of mass spectrometer do you have?

For most mass spectrometers, when you export a collision energy optimization method, there will be multiple entries corresponding to different collision energies for a single transition. The Q3 values for the individual entries will differ by 0.01 units. When Skyline is reading chromatograms from a raw file, Skyline notices when there is a group of transitions whose Q3 values have this 0.01 stepping, and Skyline uses this to recognize that this is a group of CE optimization chromatograms for the same transition.

In older versions of Skyline, Skyline would sometimes not care about whether there was this 0.01 difference between the Q3 values. Sometimes, even if the chromatograms all had the same Q3 value, Skyline would still consider that these chromatograms belonged together, and assumed that the collision energy steps were in the same order that the chromatograms were found in the raw file.

In Skyline 23.1 the behavior was changed so that Skyline is more strict about requiring this 0.01 difference in order to recognize that chromatograms belong to a collision energy set.

The usual reason that collision energy optimization stopped working for someone in Skyline 23.1 is that the Q3 values were not what Skyline was expecting, but it is also possible that something else is going wrong.

If we could see your Skyline document and some of your raw files we could probably figure out what is going wrong.
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.
In Skyline 23.1 there is a new "Include results files" checkbox on the "Share Skyline Document" dialog which you can use to include your raw files in the .zip file, or you could package those up separately.

Files which are less than 50MB can be attached to this support request. You can upload larger files here:

It would be very helpful if you could send us your Skyline document and raw files so that we can make sure we understand what has gone wrong for you.
-- Nick