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/

When you do the DIA section, it uses a DIA-NN .speclib file with a report.tsv file, which represents a search of DIA data. Currently this workflow assumes the mProphet workflow where the user is first building a spectral library from a prior experiment, and then using it for a de novo search of separate DIA runs with decoys for q value estimation and possibly training a new mProphet model.

In the case where the library step generates a library with peak boundaries, we should be suggesting chromatogram extraction from those files, if we can find them, just as we currently do for DDA. If we also include the checkbox to exclude search files, then a user who wants the old behavior even when they have built their library from DIA-NN or EncyclopeDIA results can check the checkbox to add files of their choosing.

Ideally, if a user goes straight through accepting extraction from the files searched by DIA-NN or EncyclopeDIA, we should also suggest not adding decoys in the final FASTA page.