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Failed importing DIA-PASEF results and isolation schemes msielaff  2021-09-02 07:28
 
Dear Skyline team,

I'm trying to set up a Skyline document for a AutoQC-Panorama pipeline in order to monitor some peptides as QC from HeLa DIA-PASEF runs. Unfortunately, Skyline fails to import the results from some of our DIA-PASEF methods with following error:

At 3:23 PM:
Failed importing results file 'O:\RAW_ttp\O210827_003_Slot1-1_1_3239.d'.
error reading spectrum merged=12 frame=5 scanStart=735 scanEnd=937
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'O:\RAW_ttp\O210827_003_Slot1-1_1_3239.d'.
error reading spectrum merged=12 frame=5 scanStart=735 scanEnd=937 ---> System.Reflection.TargetInvocationException: error reading spectrum merged=12 frame=5 scanStart=735 scanEnd=937 ---> System.Exception: error reading spectrum merged=12 frame=5 scanStart=735 scanEnd=937 ---> System.Exception: Scan number [936] out of range.
   at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, DetailLevel detailLevel)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetCachedSpectrum(Int32 scanIndex, DetailLevel detailLevel) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1155
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 spectrumIndex) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 893
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1075
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1126
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.Read() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 953
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.<RunAsync>b__33_0() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 810
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1940
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.NextSpectrum() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 916
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 259
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 239
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList`1 chromatogramRequestOrder) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 592
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 384
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 252
   --- End of inner exception stack trace ---



Skyline also fails when I try to import the isolation scheme from the raw file:

---------------------------
Skyline
---------------------------
Failed reading isolation scheme.
Scan number [936] out of range.
---------------------------
OK More Info
---------------------------
System.Reflection.TargetInvocationException: Scan number [936] out of range. ---> System.Exception: Scan number [936] out of range.
   at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, DetailLevel detailLevel)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetCachedSpectrum(Int32 scanIndex, DetailLevel detailLevel) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1155
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 spectrumIndex) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 893
   at pwiz.Skyline.Model.IsolationSchemeReader.ReadIsolationRanges(MsDataFileUri dataSource, IsolationRange[] isolationRanges) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\IsolationSchemeReader.cs:line 159
   at pwiz.Skyline.Model.IsolationSchemeReader.ReadIsolationRangesFromFiles(IProgressMonitor progressMonitor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\IsolationSchemeReader.cs:line 62
   at pwiz.Skyline.Model.IsolationSchemeReader.Import(String name, IProgressMonitor progressMonitor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\IsolationSchemeReader.cs:line 44
   at pwiz.Skyline.SettingsUI.EditIsolationSchemeDlg.<>c__DisplayClass74_1.<ImportRangesFromFiles>b__1(IProgressMonitor progressMonitor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\SettingsUI\EditIsolationSchemeDlg.cs:line 1045
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 254
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1940
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.SettingsUI.EditIsolationSchemeDlg.ImportRangesFromFiles(MsDataFileUri[] dataSources) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\SettingsUI\EditIsolationSchemeDlg.cs:line 1045
 ---------------------------


Based on these error messages, do you have any idea what the problem could be and how to solve it?

Many thanks,
Malte
 
 
Nick Shulman responded:  2021-09-02 07:42
I do not think we have seen that error before, but it looks like Skyline might be confused about how many spectra there are supposed to be.

Can you send us your raw file? It would probably also be helpful for us to see your Skyline document.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.

Please also create a .zip file from your "O210827_003_Slot1-1_1_3239.d" raw file folder.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here:
https://skyline.ms/files.url

This looks like it must be a bug in either Skyline or ProteoWizard. I imagine that it might be possible to work around this bug by using ProteoWizard MSConvert to convert the raw file to .mzML, or it might be that you would run into the same sort of error using MsConvert.

After we see your raw file, we will probably be able to give you a better answer as to what is going wrong.
-- Nick
 
msielaff responded:  2021-09-03 01:47
Dear Nick,

Thanks for your response. Of course - I uploaded the Skyline document and raw files to the File Sharing Folder.

Skyline document: 20210804_AutoQC_Test2.sky.zip
Raw file: O210827_003_Slot1-1_1_3239.d.zip

In addition, I uploaded another DIA-PASEF raw file which caused no problems: G210721_006_Slot1-9_1_2274.d.zip

Best regards,
Malte
 
Matt Chambers responded:  2021-09-08 14:51
Hi Malte,

I'm pretty sure this is a bug in the timsTOF acquisition software but I'm still waiting to hear back from Bruker about it. In the meantime it was pretty easy to work around it by never letting the DIA windows' end scan go past the number of scans in the frame. Importing your file seems to work fine for me now. The fix will be in the next daily or you can get in from the bleeding edge build in this zip file:
https://teamcity.labkey.org/guestAuth/repository/download/bt209/1531509:id/SkylineTester.zip

Thanks for providing your files!
-Matt
 
msielaff responded:  2021-09-09 04:09
Hi Matt,

No problem and thanks a lot for taking care and providing a workaround so quickly!

Best wishes,
Malte
 
Antoine responded:  2021-10-01 03:48
Hi Matt,

Is it possible to get build in the zip? The link is broken.

I have a very similar problem, I think:


error reading spectrum merged=2 frame=2 scanStart=660 scanEnd=919
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'M:\Public_Files\tmp\2Antoine\1fastprisma\dia_PQ500-A4eq_100min_Slot2-28_1_4841.d'.
error reading spectrum merged=2 frame=2 scanStart=660 scanEnd=919 ---> System.Reflection.TargetInvocationException: error reading spectrum merged=2 frame=2 scanStart=660 scanEnd=919 ---> System.Exception: error reading spectrum merged=2 frame=2 scanStart=660 scanEnd=919 ---> System.Exception: Scan number [918] out of range.
   at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, DetailLevel detailLevel)
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetCachedSpectrum(Int32 scanIndex, DetailLevel detailLevel) in C:\proj\pwiz_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1155
   at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 spectrumIndex) in C:\proj\pwiz_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 893
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1075
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1126
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.Read() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 953
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.<RunAsync>b__33_0() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 810
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1940
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.NextSpectrum() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 916
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 259
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 239
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList`1 chromatogramRequestOrder) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 592
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 384
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 252
 
Matt Chambers responded:  2021-10-01 07:28
This link should stay valid: https://teamcity.labkey.org/guestAuth/repository/download/bt209/lastSuccessful/SkylineTester.zip
 
Antoine responded:  2021-10-01 07:45
Hi thank you,

How does it work? If I double click the .exe file it will patch Skyline Daily?
Best
 
Matt Chambers responded:  2021-10-01 07:51
There's a standalone distribution of Skyline-daily in there. It won't replace/interfere with any other version on your computer. It should run as-is without any installation needed.