Dear Skyline-Team,

I have the following situation:
I set up a PRM experiment to optimize CE for my synthetic peptides and labeled reference peptides by running them at different CEs in different injections (15 raw files - each run acquired with a different CE value).
Now, from visual inspection, I can determine at which CE the peak area is highest and a CE which results in my prefered transition rank distribution (e.g. sometimes the highest area comes from y1 or y2 fragments which I would like to exclude from analysis).
So now, I would like to include the spectra from my preferred CE setting into a spectral library - for each peptide this could be different of course - sometimes I want to optimize for area, sometimes for transitions.
What would be the best option to do that?
If I just "Build" a library from my combined dataset, there is no way to influence which spectra will be added to the library.
Could you point me in the right direction? Maybe I am missing something here ...
I know from the tutorial that I can automatically let Skyline optimize CE values, but as far as I understood it does that only for "Area", which sometimes is not something I want to do.
Thank you very much in advance!

Best,
Max