Error thrown during DIA-Umpire processing step

Error thrown during DIA-Umpire processing step edf4n  2021-10-04

PC running Windows 10 Pro for Workstation
Version of Skyline: (9b557b3b8)

Hello all!
I am looking for help trying to decipher this error that occured when trying to run the DIA-Umpire process in Skyline

System.IO.IOException: Error occurred running process.
Command-line: C:\Users\Erin Jeffery\AppData\Local\Apps\2.0\339HZP6L.A8J\H0P5GENV.PDC\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\msconvert -v --32 -z --mz5 -o "C:\Users\Erin Jeffery\AppData\Local\Temp" --outfile 3wdl2dwq.iuq.mz5 --filter "diaUmpire params=C:\Users\Erin Jeffery\AppData\Local\Temp\fyciffec.5ha.params" "C:\Users\Erin Jeffery\Downloads\SkylineDIA_210927\210901_Jurkat1_tryp_DIA_4hr_Fr4.raw"
Working directory:
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 65
at pwiz.Skyline.Model.DiaUmpireDdaConverter.Run(IProgressMonitor progressMonitor, IProgressStatus status) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\DiaUmpireDdaConverter.cs:line 139

Is Skyline looking for msconvert that is in a different path? I don't have much experience with troubleshooting error codes. Any help is appreciated!

Nick Shulman responded:  2021-10-04
Skyline ships with its own copy of msconvert.exe, in the same folder as Skyline.exe.

Your error seems to indicate that msconvert.exe was found and executed, but ran into some problem doing what it was supposed to do.

If you send us your Skyline document and raw files, we can try to reproduce the problem and figure out what is going wrong.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files like libraries or extracted chromatograms. The raw files are not included in the .zip file, so you should be sure to also send us your raw files. I am not sure, but maybe we will also need your FASTA file, if you specified one in the Import Peptide Search wizard before you hit this error.

If that .zip file and you raw files are less than 50MB you can attach them to this support request.
Otherwise, you can upload them here:

It would also be helpful if you could send us a screenshot of what you have chosen in the "Import Peptide Search" pages as that will make it easier for us to duplicate the steps that you did.

-- Nick
edf4n responded:  2021-10-07
Thanks Nick.
I have uploaded the files you requested.

Just to let you know, this issue is specific to the computer that I am using. It also happens to be a computer running Proteome Discoverer. Could there be some kind of path confusion due to the presence of Proteome Discoverer?

I see that a new version of Skyline was released. I may try again with the new version
Nick Shulman responded:  2021-10-07
I cannot think of a reason that Proteome Discoverer might be messing anything up. Skyline is definitely running the msconvert.exe which ships with Skyline.

You error message mentions the file "C:\Users\Erin Jeffery\AppData\Local\Temp\fyciffec.5ha.params". If that file is still on your computer, please attach it to this support request. That file contains the parameters indicating what Skyline is telling msconvert.exe to do.

If that file is no longer on your computer, can you try to reproduce the error again, and send us the new .params file that gets mentioned?

If you are not able to send us a .params file, then we might need more information to reproduce this bug. What did you specify as an isolation scheme when you did "File > Import > Peptide Search"?
-- Nick
edf4n responded:  2021-10-07
Dear Nick,
Here is the .params file that you requested!
Thank you for your assistance.

Nick Shulman responded:  2021-10-07

Thank you for sending that .params file.
I cannot get msconvert to do anything like what you are seeing.
I am hoping this problem will disappear when you upgrade to the newer Skyline. If anything weird has happened to your Skyline installation, those problems will probably be fixed when you install a new Skyline version.
Also, we will be releasing a new update of Skyline-Daily probably later this week, and you can try that too.

Usually when msconvert is running as part of the dia umpire search, there is a lot of output displayed to you in the Import Peptide Search wizard window. Is there any sort of output like that that you could send us that might give indicate what the error is?
-- Nick