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Waters Xevo G2 QTof raw file error

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Waters Xevo G2 QTof raw file error bruce37661  2024-11-17 18:17
 

Hi, I am new to Skiline and beleive I must be missing something when importing my raw file. I can open the file in MassLynx with a problem, however, the file looks like it is importing up until the very end and then gives the error message.

At 6:07 PM:
Failed importing results file 'C:\Users\RobertRegister\Dropbox\Skyline\Tocilizumab 61 min scan.raw'.
error reading spectrum function=1 process=0 scan=24757
Under More Info it says

At 6:07 PM:
Failed importing results file 'C:\Users\RobertRegister\Dropbox\Skyline\Tocilizumab 61 min scan.raw'.
error reading spectrum function=1 process=0 scan=24757
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'C:\Users\RobertRegister\Dropbox\Skyline\Tocilizumab 61 min scan.raw'.
error reading spectrum function=1 process=0 scan=24757 ---> System.Reflection.TargetInvocationException: error reading spectrum function=1 process=0 scan=24757 ---> System.Exception: error reading spectrum function=1 process=0 scan=24757 ---> System.Exception: [pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: EOF Scan File Read Error
at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, DetailLevel detailLevel)
at pwiz.ProteowizardWrapper.MsDataFileImpl.GetCachedSpectrum(Int32 scanIndex, DetailLevel detailLevel) in C:\proj\skyline_24_1\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1384
at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 spectrumIndex) in C:\proj\skyline_24_1\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 995
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1109
--- End of inner exception stack trace ---
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1160
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.Read() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 987
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.<RunAsync>b__33_0() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 845
--- End of inner exception stack trace ---
at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Util\Util.cs:line 1926
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.NextSpectrum() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 950
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 273
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 253
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList`1 chromatogramRequestOrder) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 617
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 388
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 256
--- End of inner exception stack trace ---
Any idea what is going on? Also, it says Chomatogram information unavailable.

Any help would be appreciated !! Bruce
 
 
Nick Shulman responded:  2024-11-17 19:13
We have not seen the error "EOF Scan File Read Error" before, but that sounds like the sort of error that you would get if the .raw file that you were trying to read was corrupted, or, specifically, was shorter than it was supposed to be.

Is "Tocilizumab 61 min scan.raw" the only file that you have, or could you try this with a different file?
It's possible that the file corruption happened when you were copying that file to your computer. It might be that if you copied the file again from its original location you might end up with a file that you can read.

If you want a simpler way to look at the spectra and chromatograms in a .raw file, you can install ProteoWizard.
When you install ProteoWizard, one of the programs that appears on the Windows Start Menu is "SeeMS" which you can use to look at raw data files.
You can install ProteoWizard from here:
https://proteowizard.sourceforge.io/download.html

My guess is that if you were to look at this file using SeeMS.exe, you would see the same error.

Your error message says it was unable to read scan #24757.
Do you have some Waters software that you can use to look at that file? Let us know if you are able to use other software to look at all of the spectra in that file, because that would mean that the data is not corrupted, and there might be a bug in our software that we need to fix.
-- Nick
 
bruce37661 responded:  2024-11-17 19:43
Hi Nick, I am getting this error with several files. I did try to recopy it and had the same problem. I can open them in MassLynx and BiopharmaLynx 1.3.5 without a problem. I am happy to send you a file to try yourself if it will help. Bruce
 
Nick Shulman responded:  2024-11-17 19:51
Yes, it would be helpful if you could zip those files and upload them here:
https://skyline.ms/files.url
--Nick
 
Nick Shulman responded:  2024-11-19 10:00
Thank you for uploading that .raw file folder.
I cannot get anything bad to happen with it.
I have no trouble telling Skyline to extract chromatograms from all of the spectra.

I see that your file is in your "DropBox" folder. I wonder if DropBox is doing something weird which is causing a problem.

If you would like, you could send us the rest of your .raw files as well as screenshots of the steps that you are doing in Skyline.
We could then do those same steps, and either we will run into the same error as you or we will be able to send you the Skyline document that you would have ended up with if you had been successful.
-- Nick