Is it possible to optimise % HCD and % CID collision energies

support
Is it possible to optimise % HCD and % CID collision energies alan atkins  2024-11-20 12:25
 

Similar to the existing routine for optimizing CE on a triple quad, is it possible to optimise % HCD and/or % CID on a Thermo Stellar MS?

 
 
Nick Shulman responded:  2024-11-20 13:01
Yes. "PRM CE Optimization" first became available in Skyline 23.1.
There is some information about how to use it here:
https://skyline.ms/announcements/home/support/thread.view?rowId=63211
-- Nick
 
alan atkins responded:  2024-11-25 22:37
Hi,
I've tried to set up a NCE optimization method for a Stellar MS, but when I select Stellar MS, the optimization box is greyed out.
I was hoping to be able to create an isolation list rather than having to use a method template. I don't have instrument drivers on my laptop
 
Nick Shulman responded:  2024-11-25 23:19
A few months ago someone noticed that the Export Isolation List dialog only allows you to optimize collision energy for a couple of instruments:
https://skyline.ms/announcements/home/support/thread.view?rowId=65116

It seems that I even made them a special build of Skyline which allows you to optimize collision energy for all instruments:
https://proteome.gs.washington.edu/~nicksh/SpecialSkylines/PrmCeOpt/

This special build of Skyline is a few months out of date so it might not be able able open documents created by the latest version of Skyline-daily, but it should be able to handle documents created by Skyline 24.1. If you have Skyline-daily and need to create something which is compatible with Skyline 24.1 you can use the "File > Share" menu item and choose an older version of Skyline in the "Skyline file format" dropdown.

I do not know whether this special build of Skyline actually fixes the problem, but it might work for you.

If there is still something wrong after using this special build of Skyline, such as that the collision energy values are all the same even though they are supposed to be different on each line, then please send us your Skyline document.
You can use the "File > Share" menu item in Skyline to create a .zip file containing your Skyline document and supporting files.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick