collision energy QTRAP 6500

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collision energy QTRAP 6500 viragsagikiss  2019-02-28
 

Dear Skyline Team,

I find the collision energy optimisation option and tutorial very useful! Great work and looking forward using it.
Following your tutorial on https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/SmallMoleculeMethodDevCEOpt.pdf I have 2 questions.

where do you get your data for converting CE between Waters and ABSCIEX instruments? I m looking for QTRAP 6500. And how do i upload them to the CE equation editor? Apologies, it might be obvious but i can't find it. In the Edit Collision Energy Equation you have 2 lines, one corresponding charge 2 and the below one for charge3.

Charge slope intercept
2 something something
3 something something

Again, apologies if this question has been answered.
Virag

 
 
Brian Pratt responded:  2019-02-28
Hi Virag,

There's no conversion formula, it's determined experimentally.

The tutorial https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_optimize_ce goes into some detail - it's in terms of peptides but the same principles apply.

Thanks for using the Skyline support board!

Brian Pratt