DIA Umpire error

DIA Umpire error kongdezhi  2021-07-12

I am setting up a DIA analysis workflow using DIA raw to build a library. I met a error message about MSconvert (error 1).
System.IO.IOException: Error occurred running process.
Command-line: H:\20210708-TPP-ZQN\msconvert -v --32 -z --mz5 -o "C:\Users\PC\AppData\Local\Temp" --outfile sz44e0ox.pqm.mz5 --filter "diaUmpire params=C:\Users\PC\AppData\Local\Temp\1afneglc.puq.params" "H:\20210708-TPP-ZQN\TPP-Huh7-1-0.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

Then I install Skyline in another PC, I met a new error (error 2) as followed:
System.ComponenModel.win32Exception (Ox80004005): The system cannot find the file specified
at sytem Diagnostics Process.StartWithCreateProcess (ProcessStartInfor startinfo)
at System Diagnostics Process.Start (ProcessStartInfor startinfo)

Please advise ? it is so difficult to solve the errors by myself. thanks

Matt Chambers responded:  2021-08-12

Hi Dezhi,

It looks like Skyline is somehow using an msconvert in a TPP install. That's pretty weird and may have something to do with your system PATH. But Skyline should not be using an msconvert in your PATH, it should only work with the msconvert installed alongside Skyline. I'm on leave right now but when I get a chance I'll try to reproduce that.

In the meantime you can probably fix it by removing TPP from your path, if that's an option (it may break the TPP though, or any scripts you have that use it).

The error you get on another PC is less informative. Do you get that error every time? Is there any more information available? Is it a ClickOnce install (installed from website) or an admin install (installed from an MSI file)?