The tutorial at this link:
https://panoramaweb.org/_webdav/MacCoss/Courses/%40files/2024-09%20BMSS/Tutorials/TUM-Tutorial/SkylineTutorial_ENB_09032024.pdf

With files at:
https://panoramaweb.org/_webdav/MacCoss/Courses/%40files/2024-09%20BMSS/Tutorials/TUM-Tutorial/

Walks the reader through the Import DIA Peptide Search wizard. When it reaches the full-scan settings, the MS/MS isolation scheme field is set to "Results only" which would actually be wrong for these files, because they use the classic SWATH 0.5 m/z margin. Switching to "Results (0.5 margin)" would probably work, but it would not allow them to check the checkbox "Use DIA precursor window for exclusion" which they also seem to want to do.

At this point in the wizard, the user has specified the chromatogram extraction files, and we could easily offer to automatically generate an accurate prespecified isolation scheme, which is what the tutorial walks them through manually next. Another advantage of at least looking at the isolation scheme(s) in the files at this point is that it would allow us to detect issues like not specifying a margin when one clearly exists or specifying raw data with staggered windows, where we should advise the user to use msConvert to deconvolute the staggered windows before the import.

It would be more expensive, but it we looked at all of the imported files we would be able to tell the user if they do not all contain the same isolation scheme.