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!