George Rosenberger

Thanks for the feedback! We have been using similar workarounds before. FragPipe also uses similar mechanisms for very large databases.

This will be a super useful addition, thanks for working on this. We should try to replace all data intensive output tables with parquet files and implement plug-and-play support in...

Usually SWATH2stats expects the output to be processed by TRIC. You can also apply TRIC to a single file, it will just filter the results to the selected cutoffs and...

Are you sure? I think this is implemented after the following calculation: https://github.com/OpenMS/OpenMS/blob/b7f3d1bb456f17a7c4ae42b20721bbfdf70e9ce3/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp#L624

I'm unfortunately still not sure if I understand the problem. I think the following is happening: - OpenSWATH uses assay iRT and then first transforms this to assay RT. -...

I believe delta RT is computed also in experimental time: https://github.com/OpenMS/OpenMS/blob/b7f3d1bb456f17a7c4ae42b20721bbfdf70e9ce3/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp#L756 What might be confusing is that expected_rt is first obtained in [library space](https://github.com/OpenMS/OpenMS/blob/b7f3d1bb456f17a7c4ae42b20721bbfdf70e9ce3/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp#L536) and then transformed to [experimental space](https://github.com/OpenMS/OpenMS/blob/b7f3d1bb456f17a7c4ae42b20721bbfdf70e9ce3/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp#L539)....

Looks great, thank you! Please feel free to merge when you think that it is ready.