Cannot import timsTOF PASEF bbCID data

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Cannot import timsTOF PASEF bbCID data michael witting  2021-10-01
 

Dear Skyline team,

I recently acquired in collaboration with Bruker some lipidomics data on the timsTOF pro, but I cannot read it into Skyline. I'm getting the following error:

At 13:42:
Failed importing results file 'H:\Data_Bruker\21010929_Celegans_ttPro\HESI - RP\neg bbCID\HESI_Celegans_MTBE-2_150ul_bbCID_4ul_neg_19_1_3206.d'.
[Reader_Bruker::createInstrumentConfigurations] no case for InstrumentSource 18
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'H:\Data_Bruker\21010929_Celegans_ttPro\HESI - RP\neg bbCID\HESI_Celegans_MTBE-2_150ul_bbCID_4ul_neg_19_1_3206.d'.
[Reader_Bruker::createInstrumentConfigurations] no case for InstrumentSource 18 ---> System.Exception: [Reader_Bruker::createInstrumentConfigurations] no case for InstrumentSource 18
bei pwiz.CLI.msdata.ReaderList.read(String filename, MSData result, Int32 runIndex, ReaderConfig config)
bei 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\pwiz_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:Zeile 197.
bei pwiz.Skyline.Model.Results.MsDataFilePath.OpenMsDataFile(Boolean simAsSpectra, Boolean preferOnlyMs1, Boolean centroidMs1, Boolean centroidMs2, Boolean ignoreZeroIntensityPoints) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\MsDataFilePath.cs:Zeile 291.
bei pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:Zeile 188.

Thanky you very much for your help.

Best regards,

Michael

 
 
Brian Pratt responded:  2021-10-01

Hi Michael,

That sounds like it must be some data file format variant we haven't seen before.

Can you upload your Skyline file (use File>Share>Complete to create a .sky.zip file) and the HESI_Celegans_MTBE-2_150ul_bbCID_4ul_neg_19_1_3206.d file as well? We'll have a look at this and see what we can do. You can upload to http://skyline.ms/files.url or we can arrange something private if you prefer.

Thanks for using the Skyline support board!

Brian Pratt

 
michael witting responded:  2021-10-01

Dear Brian,

I'm currently uploading the data file. In parallel I checked another data file from the same analysis batch. This file worked. The difference was that the working file was collected with a standard ESI, while the one that didn't work used the new VIP-HESI source.

Maybe that helps?

Best regards,

Michael

 
michael witting responded:  2021-10-04

Dear Brian,

indeed the problem is the ion source. I could change with the help of Bruker the parameter in their .tdf file using the SQLiteBrowser. Changing the entry from 18 (=VIP-HESI) to 1 (=ESI) for the ion source helps. However, a new error appears:

At 09:49:
Failed importing results file 'K:\HESI_Celegans_MTBE-2_150ul_bbCID_4ul_neg_19_1_3206.d'.
error reading spectrum merged=170 frame=171 scanStart=1 scanEnd=1001
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'K:\HESI_Celegans_MTBE-2_150ul_bbCID_4ul_neg_19_1_3206.d'.
error reading spectrum merged=170 frame=171 scanStart=1 scanEnd=1001 ---> System.Reflection.TargetInvocationException: error reading spectrum merged=170 frame=171 scanStart=1 scanEnd=1001 ---> System.Exception: error reading spectrum merged=170 frame=171 scanStart=1 scanEnd=1001 ---> System.IO.InvalidDataException: Unable to determine isolation width for the scan targeted at 150
bei pwiz.Skyline.Model.Results.SpectrumFilter.CalcDiaIsolationValues(SignedMz& isolationTargetMz, Nullable1& isolationWidth) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectrumFilter.cs:Zeile 1235. bei pwiz.Skyline.Model.Results.SpectrumFilter.FindFilterPairs(IsolationWindowFilter isoWin, FullScanAcquisitionMethod acquisitionMethod, Boolean ignoreIsolationScheme) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectrumFilter.cs:Zeile 1117. bei pwiz.Skyline.Model.Results.SpectrumFilter.HasProductFilterPairs(Nullable1 retentionTime, IList1 precursors) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectrumFilter.cs:Zeile 1009. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 1064. --- Ende der internen Ausnahmestapelüberwachung --- bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 1129. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.Read() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 956. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.<RunAsync>b__33_0() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 813. --- Ende der internen Ausnahmestapelüberwachung --- bei pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:Zeile 1940. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.NextSpectrum() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 919. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 262. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 242. bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList1 chromatogramRequestOrder) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 595.
bei pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:Zeile 384.
bei pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:Zeile 252.
--- Ende der internen Ausnahmestapelüberwachung ---

Best regards,

Michael

 
Brian Pratt responded:  2021-10-04

Thanks for the update. You are correct about the initial issue, that's an ion source that is not mentioned in the current Bruker SDK, we will add support for that. Your workaround should be fine for now.

Meanwhile, I am investigating the "error reading spectrum merged=170 frame=171 scanStart=1 scanEnd=1001" problem.

Thanks

Brian

 
Brian Pratt responded:  2021-10-05

There are some curious things going on in that file, may I have your permission to use it as an input to an automated test? (This would make the file public to anyone that cared to dig around in our public build system.)

Specifically we were tripping up on the presence of a TriggerMass value in the all ions MS2 scans, which implies a more DDA-like operation (or, at least, that's how our code was handling it). Is this intentional?

Best regards,

Brian

 
michael witting responded:  2021-10-06

No problems in sharing the file. I asked Bruker also about the TriggerMass etc. It is tims bbCID data, so it switches between low and high energy experiments. What is the trigger mass? I would guess something from the middle of the mass range.

 
Brian Pratt responded:  2021-10-06

Thanks for your help with this. The problem will be corrected in our next Skyline-Daily release, and for now if you'd like to test the fix you can download https://teamcity.labkey.org/guestAuth/repository/download/bt209/.lastSuccessful/SkylineTester.zip and just run Skyline-Daily.exe from whatever directory you unzipped to. (There's no installer, and it won't interfere with your existing Skyline installation.)

Best regards,

Brian

 
michael witting responded:  2021-10-07

Dear Brian,

thank you very much. Unfortunately, even the SkylineTester it doesn't work, but maybe I need to way for the daily build.

Best regards,

Michael

 
Brian Pratt responded:  2021-10-07

Is it failing the same way, or something new?

It's probably just your settings needing a tweak. See attached for a screenshot of what I see with your file using that downloaded build. The .sky file in your original post didn't have the full scan settings ready to go, so that's probably all this is.

Best regards,

Brian

 
michael witting responded:  2021-10-07

Now it works! Sorry for my ignorance on the settings ;-).
Just got the data from Bruker and wanted to make it work without thinking too much about settings.

Thank you very much!

 
Brian Pratt responded:  2021-10-08

Excellent! Thanks for helping us improve Skyline.