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Can different scan filters (e.g. HCD or CID) of the same precursor be separated?

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Can different scan filters (e.g. HCD or CID) of the same precursor be separated? alan atkins  2024-11-20 12:31
 

If data has been acquired using an acquisition method that uses both HCD (beam type fragmentation in a collision cell) and CID (Resonant fragmentation in an Ion Trap) on the same precursor, can those filters be separated in Skyline? Currently, when I try to process with Skyline, it treats the MS2 fragments the same, so the you get a noisy combined XIC.
 
 
Nick Shulman responded:  2024-11-20 12:59
Yes. You can right-click on a Precursor in the Targets tree and choose "Edit Spectrum Filter".
There is some information about this relatively new feature here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=SpectrumFilters

Also, in Skyline-daily, on the "Instrument" tab at "Settings > Transition Settings" there is a "Advanced filtering" box where you can define a spectrum filter which is applied to everything in the document.
-- Nick