Issue 894: Make "Use Results" isolation scheme work for Import > Peptide Search of DIA

issues
Status:open
Assigned To:Kaipo Tamura
Type:Todo
Area:Skyline
Priority:2
Milestone:22.2
Opened:2022-07-06 by Brendan MacLean
Changed:2022-07-20 by Brendan MacLean
Resolved:
Resolution:
Closed:
2022-07-06 Brendan MacLean
Title»Make "Use Results" isolation scheme work for Import > Peptide Search of DIA
Assigned To»Kaipo
Notify»Mike MacCoss
Type»Todo
Area»Skyline
Priority»2
Mike pointed out that the lab finds using the Import Peptide Search wizard for DIA cumbersome, because it requires the user to specify the isolation scheme explicitly. This is because we felt we would need it for the step where we insilico-digest the FASTA sequences and decide which should be added to the Targets list. For a DDA library that covered 50 to 2000, we might need to exclude a lot of precursors if the isolation scheme turns out to be 400 to 800.

Still, it is obviously desirable to allow users to have Skyline work this out automatically, and Mike pointed out that it is still easy to mistakenly choose the wrong isolation scheme and get very confusing results.

So, I think we should 1:
- Add more checking during import of DIA data that the isolation scheme resembles what the user prespecified if one is prespecified. Error if an isolation window match does not match the isolation scheme specification? I think we want to allow the data to contain a superset of what is specified in the isolation scheme. The most dangerous case is when we assign an isolation window from the isolation scheme that does not match what is in the data file.

- In the wizard, allow "Automatic" and automatically generate a prespecified isolation scheme from the import data specified by the user.

Mike also notes that in combination with EncyclopeDIA or any DIA-based search engine, the library matches will only be in the isolation range. So that the problem we are defending against with the current implementation is not an issue for this use case.

2022-07-20 Brendan MacLean
Milestone»22.2