Collision Energy Optimization for Precursors? philip remes  2020-10-09

I've done the tutorial the does collision energy optimization by exporting transition lists:
For small molecules, it would be useful to do the same thing for PRM experiments. But the Optimizing Dropdown box is disabled for File->Export->Isolation list, even though I see it for the Export->Transition List option. Is this a feature that could be added?


Nick Shulman responded:  2020-10-09
I imagine this would be difficult to support.

Skyline disables the "Optimizing" dropdown if the instrument is a full scan instrument (which it always is when doing "Export > Isolation List").

When Skyline exports an optimizing transition list for a triple quad, Skyline outputs a set of transitions with different values of the optimization parameter and where the Q3 values differ by 0.01.

When you import results from a SRM file and indicate that you are optimizing something, Skyline notices when there is a set of chromatograms with identical Q1 values and where the Q3 values differ by 0.01, and Skyline assumes that that set of chromatograms had a series of different values for the optimization parameter.

I believe the reason that the method gets exported like that is that Skyline does not know how to look at the chromatograms in a raw file and know what their CE or other optimization parameter value was.

I could imagine that we could make this same sort of thing work for isolation lists and full scan mass spectrometers, but I think it would be a fair amount of work.

This is an interesting question and someone else might have a different idea about how much work this would be.
-- Nick
philip remes responded:  2020-10-12
Thanks for the response and analysis Nick. I do think that such a tool for optimizing full scan mass spectrometer parameters like CE, CV, DP would be more and more useful as small molecule analysis in Skyline becomes more important.