Collision Energy (CE) Optimization for PRM

Collision Energy (CE) Optimization for PRM minsu907  2024-01-19 10:28

Dear Skyline team,

We are trying to optimize CE for our PRM.
We could find a tutorial for CE optimization, but it only covers MRM using QQQ.

Could you let us know if CE optimization for PRM is feasible on Skyline program?

Minsoo Son

Nick Shulman responded:  2024-01-19 10:39
Yes, Collision Energy Optimization for PRM is a new feature that first became available in Skyline 23.1.

Which type of mass spectrometer do you have?

The way to use the feature is to use the "File > Export > Method" menu item in Skyline and then choose "Collision Energy" in the "Optimizing" dropdown.
What is new in Skyline 23.1 is that the "Optimizing" dropdown is available on more types of instruments. In earlier versions of Skyline that dropdown was only enabled when exporting a method for a triple quad.

The rest of the way that you do collision energy optimization is the same as the old way for triple quads. You tell Skyline how the collision energies should vary across the optimization steps by going to "Settings > Peptide Settings > Prediction" and editing the thing in the "Collision Energy" dropdown.

Also, when importing results with the "File > Import > Results" menu item, you must choose "Collision Energy" in the "Optimizing" dropdown in the Import Results dialog.

Several people have successfully performed collision optimization on a few different types of instruments.

Let us know if you get stuck anywhere.
-- Nick
minsu907 responded:  2024-01-19 10:59

Hi Nick,

Thanks for a prompt response.

We are using the Orbitrap Exploris series. Of course, we will definitely try and let you know if we have any issues.
Just one quick question. Is this feature also available for optimizing other parameters of Orbitrap instruments, such as isolation width, RF lens frequency, etc?

Thanks for your help.


Nick Shulman responded:  2024-01-19 22:47
With PRM data, the thing that Skyline supports is collision energy optimization.

With SRM (triple quad) data, you can do optimization on either collision energy or compensation voltage.
-- Nick