Add optimized CE's to peptides in the Skyline document

Add optimized CE's to peptides in the Skyline document Astrid Guldbrandsen  2019-05-27

Dear Skyline team,

Is there a way to manually add optimized CE values to the individual peptides in the Skyline document? So that these will be in the exported isolation list instead of the default 27. I am doing scheduled PRM on a QE-HF instrument and I have optimized CE's for all the peptides, but currently I need to manually change it for all peptides in the isolation list every time I export a new one.

Best regards,

Brian Pratt responded:  2019-05-28

Hi Astrid,

You can do this in the Document Grid. Open the Transitions Report, then customize the report to include the "Explicit Collision Energy" column. You can set the values there.

Best regards,

Brian Pratt

Brian Pratt responded:  2019-05-28

Hello again,

Brendan points out that this is "Normalized Collision Energy", so we just use the values Thermo suggests (27, as you have noted).

So for now, you're stuck doing what you're doing. We could change this to use the explicit CE value as the Normalized CE value if it's available, but I'm not sure that wouldn't cause confusion. They're different ideas, really.

Thanks for using the Skyline support board,