interact-[dataname].pep.xml files from Fragpipe 19.1 can not be uploaded in Skyline

[tobimaile]

Hi all,

Thank you for your continuing work on MSFragger!

After the re-introduction of .mgf files in 3.7, I ran into a new problem with uploading files into Skyline:

While interact-.pep.xml files from 18.0 upload just fine, interact-.pep.xml files from 19.1 now have an error message in Skyline stating that there is an "Error getting a score type for this file" with a subsequent message stating that the corresponding .mgf file is required. The corresponding .mgf files are present in the directory and should be found. However when I continue on Skyline for the .mgf file search, only the .mzML files show up in the Skyline loader. Looks like something is wrong with the current .mgf files? When I load interact-.pep.xml files from 18.0, this error message does not appear.

Interestingly, the regular .pepxml files upload just fine compared to the interact-.pep.xml files in all versions of Fragpipe.

Best, Tobi