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

[fcyu]

Hi Tobi,

I reproduced your observations. Furthermore, I found that using the *.pepXML file (the one without interact- as prefix), Skyline recognized it from X!Tandem, which is OK since MSFragger uses hyperscore, and worked well. It indicates that the uncalibrated.mgf is good.

I guess some changes in interact-*.pep.xml file break Skyline. But, we did not make any big changes. I am not sure what breaks Skyline. I think it's time to create a tick to https://skyline.ms/project/home/support/begin.view . I can do that if that's OK

Best,

Fengchao

[tobimaile]

I think checking back with the Skyline team is a good idea, then it basically just gets back to walk through the interact-*.pep.xml files and see which change may break the data upload for Skyline. Comparing the general *.pepxml files at the same time may speed up things. Are there any meaningful differences/issues (besides file size) when using the .pepxml files compared to the interact-.pep.xml files when uploading on Skyline?

[fcyu]

interact-*.pep.xml files have the probability after rescoring (by PeptideProphet or Percolator), but *.pepXML files don't have it.

I have created a ticked to https://skyline.ms/announcements/home/support/thread.view?rowId=57930

Best,

Fengchao

[tobimaile]

Thank you for the update Fengchao!

Best, Tobi

[fcyu]

FYI, there are some updates in the Skyline forum: https://skyline.ms/announcements/home/support/thread.view?rowId=57930

I think the ideal solution is changing Skyline to make it support MSFragger's new change. If they don't like this idea, I will see what I can do in MSFragger. Such as renaming the mgf to _uncalibrated_uncalibrated.mgf, but it looks awkward.

Best,

Fengchao

[fcyu]

We have integrated Skyline with FragPipe. People can let FragPipe generate Skyline files seamlessly now. Contact us if you want to try the pre-released versions.

Best,

Fengchao