DIA Umpire error Francis Beaudry  2021-07-08

I am setting up a DIA analysis workflow using DIA raw to build a library. I follow the tutorial using your dataset or my dataset but I obtain the same error message. I tried on 2 different computers. Please advise ?

OK More Info
System.IO.FileNotFoundException: Le fichier 'C:\Users\franc\AppData\Local\Temp\gyo1ftie.mkn.mz5' est introuvable.
Nom de fichier : 'C:\Users\franc\AppData\Local\Temp\gyo1ftie.mkn.mz5'
   à System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
   à System.IO.File.InternalMove(String sourceFileName, String destFileName, Boolean checkHost)
   à pwiz.Skyline.Model.DiaUmpireDdaConverter.Run(IProgressMonitor progressMonitor, IProgressStatus status) dans C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\DiaUmpireDdaConverter.cs:ligne 148
matt.chambers42 responded:  2021-08-09

Hi Francis,

Sorry for the long delay. I'm the DIA Umpire integrator and I've been on paternity leave. I'm slowly getting back to work now. I'm pretty curious whether this error is due to your region/locale settings. That would be odd because we do run our tests in various locale settings (including French), but just in case, could you try running the analysis with your region/locale temporarily set to US/English?


Francis Beaudry responded:  2021-09-03

Hi Matt,
I responded by email but I guess it is not the right way to communicate.

Attached you will find screen shoot of the problem. Changing the language setting had no effect on the outcome. I tested 2 computers, with my files and your demo files provided with the tutorial and I am getting the same error. Any idea how to resolve this issue ?

Best regards,


Nick Shulman responded:  2021-09-03

Another Skyline user was getting the same error message ("FileNotFoundException" regarding a .mz file inside of "AppData\Local\Temp"):

It is likely that the problem that you are running into is identical to this other user. If that is the case, the workaround is to use ProteoWizard msconvert to generate a .mzML file which has centroided data in it.

If you are using the commandline msconvert.exe, you would use a commandline like:
msconvert.exe myrawfile.raw --filter "peakPicking true 1-"

msconvert comes with ProteoWizard which you can install from here:
-- Nick