Problem importing Agilent GCMS data to Skyline

Problem importing Agilent GCMS data to Skyline dennis jakob  2023-04-17 06:13

We would like to use Skyline to analyse our GCMS data recorded on an Agilent instrument.
When importing the data I get the following error:

At 3:22 PM:
Failed importing results file 'D:\User\djakob\GCMS\30-Test110423\S0.D'.
[ReaderFail] don't know how to read D:\User\djakob\GCMS\30-Test110423\S0.D
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'D:\User\djakob\GCMS\30-Test110423\S0.D'.
[ReaderFail] don't know how to read D:\User\djakob\GCMS\30-Test110423\S0.D ---> System.Exception: [ReaderFail] don't know how to read D:\User\djakob\GCMS\30-Test110423\S0.D
at filename, MSData result, Int32 runIndex, ReaderConfig config)
at pwiz.ProteowizardWrapper.MsDataFileImpl..ctor(String path, Int32 sampleIndex, LockMassParameters lockmassParameters, Boolean simAsSpectra, Boolean srmAsSpectra, Boolean acceptZeroLengthSpectra, Boolean requireVendorCentroidedMS1, Boolean requireVendorCentroidedMS2, Boolean ignoreZeroIntensityPoints, Int32 preferOnlyMsLevel, Boolean combineIonMobilitySpectra, Boolean trimNativeId) in C:\proj\skyline_22_2\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 197
at pwiz.Skyline.Model.Results.MsDataFilePath.OpenMsDataFile(Boolean simAsSpectra, Boolean preferOnlyMs1, Boolean centroidMs1, Boolean centroidMs2, Boolean ignoreZeroIntensityPoints) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Results\MsDataFilePath.cs:line 291
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 199
--- End of inner exception stack trace ---

Do you have an idea on how to solve this? For some reason I managed to import one file from the whole batch which is also attached.

Thank you very much,

Nick Shulman responded:  2023-04-17 07:39
In order for ProteoWizard to be able to read an Agilent .d folder, the folder needs to contain a folder named "AcqData", and that AcqData folder needs to contain files named "mspeak.bin" and "msprofile.bin".
Your folder "S0.D" does contain a folder named "AcqData" but the files "AcqData/mspeak.bin" and "AcqData/msprofile.bin" are not there.

When you are browsing for result files to import, Skyline only checks for the presence of the "AcqData" folder, which is why the "Import Results Files" dialog in Skyline allowed you to select the S0.D folder. However, because the "mspeak.bin" and "msprofile.bin" files are not in there, Skyline is unable to get any mass spectrometry data out of there.
-- Nick
dennis jakob responded:  2023-04-24 00:07
Dear Nick,
Thank you very much for your helpful response.
I actually figured that these specific files got lost in the copying process from the acquisition computer to the analysis workstation. Compressing the data folder before copying helps to avoid this data loss.
Best, Dennis