error importing fragpipe output into skyline

error importing fragpipe output into skyline jdemeter  2024-02-27 16:34


I have a similar problem to #63338: I am trying to import pep.xml files from fragpipe output for a group of DDA runs. I get the same error about not finding the scans. After doing the recommended modification of the pep.xml files, a new error occurs: please see the attached screenshot.

I am using Skyline-daily (64-bit) (a978938a7) - the previous version did not have this problem. Skyline (64-bit) is also able to read in the files without any problem.

can you please look into this?

Thank you,

Nick Shulman responded:  2024-02-27 16:52
The weird thing about your error message is that it has that line:
ERROR: F:/240223_hfd_squishome_tr/2206_CD_eWAT_Slot2-10_1_1591_calibrated
(in your screenshot, that line is split across two lines in the message box, but if you made the message box bigger I think it would all fit on one line).

What that message is trying to tell you is that BiblioSpec was looking for a file which started with a certain thing (the text that appeared on that line) and which ended with any of a list of possible extensions (.mz5, mzML, etc from an earlier part of the message).

The unusual thing is that the "F:/240223_hfd_squishome_tr/" is not supposed to appear there. It's just supposed to be saying that it's looking for "2206_CD_eWAT_Slot2-10_1_1591_calibrated", there is not supposed to be any sort of directory name there.
(The directories that it's looking in are in the later part of the message).

I am not sure why BiblioSpec is getting confused in this way, but, if you send us your files we might be able to figure it out.
You can zip everything up and upload it here:
-- Nick
jdemeter responded:  2024-02-27 18:38
Hi Nick,

Thank you for looking into this. I uploaded the folder. The pep.xml files are the originals, but the the names of the mgfs I changed from xx_uncalibrated.mgf to xx_calibrated_uncalibrated.mgf - otherwise they are not recognized.

Nick Shulman responded:  2024-02-27 22:26

Thanks for sending those files.

The thing that I was saying about how the error message shouldn't have "F:/240223_hfd_squishome_tr/" in it was completely incorrect. It's perfectly fine for the error message to have that in it-- BiblioSpec is still just looking for a file whose name starts with "2206_CD_eWAT_Slot2-10_1_1591_calibrated". It is a relatively new feature that BiblioSpec preserves the full path there in that error message.

Unfortunately, it looks like the fix that we made to fix that other support request is what is causing problems for you in the latest Skyline-daily.

That is, in your file, the attributes on the spectrum matches look like:
spectrum="2206_CD_eWAT_Slot2-10_1_1591.01130.01130.3" spectrumNativeID="1130"
Older versions of Skyline would use the "spectrum" there, but, as of the latest update of Skyline-daily, that "spectrumNativeID" value is used instead. This does not seem to be the right thing to do for your dataset.

If you were to use the slightly older Skyline-daily instead of the latest Skyline-daily then I think everything will work for you.

You can download the "unplugged" version of Skyline-daily here:

You can unzip that folder and run the older version of Skyline-daily.exe directly from where you have unzipped it. You can use this older version of Skyline-daily to import your peptide search results. After you have gotten past that step you can switch to using the latest Skyline-daily.

Thank you for reporting this issue. I will try to make sure it gets fixed soon.

By the way, I was never able to get the error that you're seeing in your screenshot to happen where it says that it could not find the spectrum file. The error that I get with the latest Skyline-daily is a bunch of things about not finding a spectrum with a particular ID.
-- Nick

Matt Chambers responded:  2024-02-28 11:40

What version of MSFragger? I may have to report this to its dev because a spectrum nativeID for MGF should be "index=<0-based index into MGF>" and it looks like it's using a 1-based index here without the correct index= prefix. In any case though I will put in a fix that will fall back to the old behavior when the spectrum source file is MGF.