Issue 981: CE optimization does not work for SCIEX QTOF instruments

Assigned To:Matt Chambers
Opened:2023-11-09 13:59 by Rita Chupalov
Changed:2023-11-09 16:14 by Nick Shulman
2023-11-09 13:59 Rita Chupalov
Title»CE optimization does not work for SCIEX QTOF instruments
Assigned To»Matt Chambers
Notify»Brendan MacLean
The issue was discovered when testing SCIEX OS method export. This is what Christie Hunter wrote:
"CEOpt is not working, it will build the method correctly but when you import the CE opt results nothing happens. There is a SxOS QTOF PCM CE_DPopt file that contains datafiles for testing and a Sky file for testing. So basically similar to how CEOpt works for QQQ, here we need to extract the fragment ion from each of the CEs and then find the tallest peak and write that as the optimal CE. I also tried DPOpt and that is working…. So that is a bit strange… but hopefully it gives you a clue. Both included in the zip file in the BOX folder."
It does not work for neither wiff nor wiff2 files. Files to reproduce the problem are in file at

2023-11-09 16:14 Nick Shulman
This works as expected in Skyline-daily, although there is no way to get it to work in Skyline 23.1.

In order to do PRM CE Optimization, you must import results from the .wiff2 file.
ProteoWizard cannot read collision energy values from the .wiff file, which is why you have to use the .wiff2 file.
This won't work in Skyline 23.1 because there is a separate bug where ProteoWizard does not properly read the isolation windows which was fixed by PR#2724.

It's currently not possible to do PRM optimization on Declustering Potential, so the only file in the dataset that would be expected to work is "062623 PCM40f sMRM CEopt 5.wiff2".

When I use Skyline-daily to import the 062623 PCM40f sMRM CEopt 5.wiff2 and specify that I am optimizing collision energy, I get the attached Skyline document.
Note that the precursor transitions end up with missing chromatograms. That will be fixed when I merge pull request #2588 into master.
 062623 PCM40f sMRM CEopt 5.wiff.scan.7z
 062623 PCM40f sMRM CEopt 5.wiff2