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Unknown error when opening LC-IMS-MS chromatograms

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Unknown error when opening LC-IMS-MS chromatograms rozas  2021-01-28
 

Hello SkyLine Team,

I would like to ask you about a problem that I have using the software ( Skyline version 20.2). The data that I want to treat was was generated with a Synapt G2-Si.

I can open the MS files when IMS was turn off but it is not possible to open the data when Ion mobility was working. The following error appears:

At 12:17 PM:
Failed importing results file 'G:\My Drive\30-REC-20-ERGO.PRO\Data\20201204-004.raw'.
[pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Generic Error

if I click in more info:

At 12:17 PM:
Failed importing results file 'G:\My Drive\30-REC-20-ERGO.PRO\Data\20201204-004.raw'.
[pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Generic Error
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'G:\My Drive\30-REC-20-ERGO.PRO\Data\20201204-004.raw'.
[pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Generic Error ---> System.Exception: [pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Generic Error
at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, Boolean getBinaryData)
at pwiz.ProteowizardWrapper.MsDataFileImpl.HasSrmSpectraInList(SpectrumList spectrumList) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1064
at pwiz.ProteowizardWrapper.MsDataFileImpl.get_SpectrumList() in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 538
at pwiz.ProteowizardWrapper.MsDataFileImpl.get_HasCombinedIonMobilitySpectra() in C:\proj\skyline_20_2_x64\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_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1430
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 216
--- End of inner exception stack trace ---

I would appreciate if you can help me.

Thank you,

have a nice day.

Laura
 
 
Brian Pratt responded:  2021-01-28

Hi Laura,

If you can share your Skyline document (use the Skyline meny item File > Share > Complete), along with the raw file, I can have a look at this.

You can upload them to http://skyline.ms/files.url or we can arrange something more private.

Thanks for using the Skyline support board,

Brian Pratt
 
rozas responded:  2021-01-28

Hello,
I have tried to attach here one of the file that I can not open but it is too large.
I can not share you the file through Skyline because it is not opened in the software, so I do not have the option to share.
Please, If you know other way to send you the file, tell me.
sorry for the inconveniences,
Thanks a lot!
Regards
 
Brian Pratt responded:  2021-01-28

Skyline's File > Share > Complete menu item will zip up your Skyline document and any supporting libraries etc into a .sky.zip file. The raw file is a separate matter.

You can upload both files to http://skyline.ms/files.url or we can arrange something more private.

  • Brian
 
rozas responded:  2021-01-29

Ok. I have attached both documents to the link that you provided to me.
thank you.

Regards.

Laura
 
Brian Pratt responded:  2021-01-29

Thanks for the files. There is something strange happening here, certainly - I can't even open that .raw file in SeeMS or msconvert.

I am wondering if it is damaged - are you able to open it in any other software, and view each scan? (Just opening it isn't a good test, you have to visit each scan the way Skyline or msconvert do.)

Best,

Brian
 
matt.chambers42 responded:  2021-01-29

Hi Laura,

You're not the first user to run into this but I've just put a fix in today so it should work in the next daily release.
 
Brian Pratt responded:  2021-02-01

Hi Laura,

Until the next Skyline Daily drops you can work around this by converting to mzML with a new copy of msconvert, which should have Matt's fix in it now.

Thanks for taking the time to let us know about the problem.

Best,

Brian Pratt
 
rozas responded:  2021-02-16

Hello,

Thank you for your nice help and collaboration,

I could open my files by using msconvert and now I can open them directly with the new beta version.

kind regards,

Laura
 
Brian Pratt responded:  2021-02-16

Excellent! Thanks for letting us know.

Best regards,

Brian