The system cannot find the file specified

The system cannot find the file specified sascha  2023-02-20 04:36

Dear Skyline people,

I am sorry in advance to haunt you with ghosts from the pasts, but I have a problem with importing Thermo Fisher raw files in one our systems by using your last version of Skyline 32-bit. We have two systems which run Windows 7 32 bit.

System 1

  • Xcalibur Foundation 3.0 SP2
  • Xcalibur 3.0
  • Q Exactive Plus Orbitrap MS 2.9

System 2

  • Xcalibur Foundation 2.0 SP1
  • Xcalibur 2.2 SP1
  • TSQ Quantum 2.3.0

I want to import an SRM run into Skyline to check system performance. While it works flawlessly with system 1, I get the following error on system 2:

At 1:15 PM:
Failed importing results file 'C:\Xcalibur\data\Faelle\Test_TSQ\230210\Test_LXQ_Q1_SRM_pos_230210.raw'.
[SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=2": [ThermoRawFile] The system cannot find the file specified.
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'C:\Xcalibur\data\Faelle\Test_TSQ\230210\Test_LXQ_Q1_SRM_pos_230210.raw'.
[SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=2": [ThermoRawFile] The system cannot find the file specified. ---> System.Exception: [SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=2": [ThermoRawFile] The system cannot find the file specified.
   at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, Boolean getBinaryData)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.HasSrmSpectraInList(SpectrumList spectrumList) in C:\proj\skyline_20_2\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1064
   at pwiz.ProteowizardWrapper.MsDataFileImpl.get_SpectrumList() in C:\proj\skyline_20_2\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 538
   at pwiz.ProteowizardWrapper.MsDataFileImpl.get_HasCombinedIonMobilitySpectra() in C:\proj\skyline_20_2\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 599
   at pwiz.Skyline.Model.Results.FileBuildInfo..ctor(MsDataFileUri msDataFileUri, MsDataFileImpl file) in C:\proj\skyline_20_2\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1430
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_2\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 211
   --- End of inner exception stack trace ---

It doesn't matter where I try to import the results file from, it is never found. Do you have any idea why this might be the case? Is the Xcalibur version on system 2 too old?

I attached the file in question and the used skyline file for you.

Thank you very much for your help!

Brian Pratt responded:  2023-02-20 08:47

That’s a tough one - can you roll back to an earlier version of Skyline that was working on that machine? We’ve pretty much stopped 32 bit development, and Win7 support.

Not the answer you’re hoping for, I’m sure. Perhaps another Skyline developer has an idea.

Best regards,
Brian Pratt

sascha responded:  2023-02-20 09:36

Thank you for your answer. The point is, that we decided to use Skyline to evaluate our system test after 32 bit development was stopped. So the first version I installed was the latest 32 bit version and I never got it to work.

Something that also puzzles me is the point that Skyline appears not to be able to find scan 2 of the file. If there was any problem with the location of the file, I'd expect it to start with scan 1.

Brian Pratt responded:  2023-02-20 10:00

Most of Skyline's interaction with the .raw file is through a library provided by Thermo, so if that's the sticking point there's not much we can do other than try to find an older release of Skyline for you to try.

The ProteoWizard tools (msconvert, SeeMS etc) use the same libraries, so it might be interesting to try viewing the file in SeeMS if there's still a 32 bit build available.

If you want to try an older version, this support thread is probably useful:

sascha responded:  2023-02-22 04:37

Good point, I installed proteowizard 3.0.23051 for x86 systems. I was able to open the file in question with SeeMS and to convert it to mzML using MSConvert.
I also installed several older versions of Skyline to check, if that makes any difference. I tested


but it didn't make any difference. Funnily, I was able to read the file with version, although it didn't yet support small molecules. That's why I had to make up some fake peptide sequence to generate a molecule list.

Anyway, since msconvert is working and I can import mzML files, my current take is to use it in a post-processing routine to call msconvert.exe to automatically convert the file to mzML.

Brian Pratt responded:  2023-02-22 08:56

Sounds like you have a path forward, excellent!