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/

Processes both a DIA dataset with Start > Import DIA Peptide Search and a DDA dataset with Start > Import DDA Peptide Search. For former produces a replicate list in the order:

DIA_01fmol
DIA_1fmol
DIA_10fmol
DIA_100fmol

While the latter produces:

DDA_01fmol
DDA_100fmol
DDA_10fmol
DDA_1fmol

And the tutorial needs to instruct the user to fix the DDA order. Presumably this is due to a difference in sorting. The former is a natural sort (presumably from our data source form) and the latter is an alphabetic sort, presumably from the DDA import code, or from the ordering inside the MaxQuant msms.txt file.

We need to fix the DDA order to use the natural sort.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.