Dear Skyline team,

I have been testing different diagonal PASEF acquisition methods using Skyline Daily (v26.1.1.083) and encountered some issues with fragment ion extraction.

I generated a SLICE PASEF method with 2 ramps and noticed gaps in the fragment ion signals in the 1/K0 dimension in Skyline that corresponded to gaps of a single ramp in my window scheme(pictures attached). I got the impression that Skyline only extracts fragment ions out of 1 ramp instead of combining data from both ramps, potentially leading to incomplete MS/MS signal representation.

I also tested synchro-PASEF methods and was wondering how the MS/MS signal extraction works there. For example if my ion population is "sliced" and is distributed in two windows/ramps, are MS/MS signals extracted from both windows or only from one?

For all analyses, I used “Use results data isolation targets” as the extraction scheme for DIA MS/MS filtering.

Thank you for your help.