Error importing Bruker xml

Error importing Bruker xml fcsigloch  2019-04-23


I tried to import a Bruker XML file of a BSA test run and got the following error message. Conversion of the same file with msconvert BSAAnalysisResults.xml gave the same error.

At 10:53:
Failed importing results file 'BSAAnalysisResults.xml'.
[SpectrumList_BTDX::HandlerCompound] Unexpected element name: fullscan

Inner exceptions:
Exception type: System.Exception
Error message: [SpectrumList_BTDX::HandlerCompound] Unexpected element name: fullscan
[SpectrumList_BTDX::HandlerCompound] Unexpected element name: fullscan
   bei pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, Boolean getBinaryData)
   bei pwiz.ProteowizardWrapper.MsDataFileImpl.HasSrmSpectraInList(SpectrumList spectrumList) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:Zeile 778.
   bei pwiz.ProteowizardWrapper.MsDataFileImpl.get_SpectrumList() in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:Zeile 475.
   bei pwiz.ProteowizardWrapper.MsDataFileImpl.get_HasSrmSpectra() in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:Zeile 742.
   bei pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:Zeile 194.

Bruker also exports mgf file format. This file could be successfully converted by msconvert BSAAnalysisResult.mgf and also searched with
java -Xmx12000M -jar r:\MSGFPlus\MSGFPlus.jar -s BSAAnalysisResult.mgf -d BSA.fasta -t 0.4Da -inst 0 -addFeatures 1 -tda 1 -e 1 -mod Mods_unlabelled.txt.
I can read in the resulting mzid file as "Peptide Search" into Skyline. When I try to read the mzML as "Results", I get another error:

At 11:04:
No scans in BSAAnalysisResults.mzML match the current filter settings.

Inner exceptions:
Exception type: pwiz.Skyline.Model.Results.NoFullScanDataException
Error message: No scans in R:\BRAIN\Testdateien_AnkeBachert\ProteinAnalysisResults_17.53-39.99.mzML match the current filter settings.
No scans in R:\BRAIN\Testdateien_AnkeBachert\ProteinAnalysisResults_17.53-39.99.mzML match the current filter settings.
   bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 363.
   bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 215.
   bei pwiz.Skyline.Model.Results.SpectraChromDataProvider.<SetRequestOrder>b__45_0() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:Zeile 556.

matt.chambers42 responded:  2019-04-23

The short version: if this is from a Bruker TOF instrument (rather than FT-ICR or trap) you should just import the raw data: the .d directory. If it's not Bruker TOF, Skyline doesn't support it.

Long version:

The first error is you trying to read a Bruker Data Analysis Exchange file, which is probably the most obscure format ProteoWizard/Skyline supports. Or at least, the file you are trying to import has the same root element as that file format (literally <root>) which is how ProteoWizard/Skyline identifies XML file types. Given the non-specificity of <root>, it's entirely possible it's a different XML format! But it could also just be an updated BTDX with new elements which break the parser. I don't actually remember whether this format supports MS1 data or just MS2. It comes from Bruker's Data Analysis software. I say Skyline supports this format but I doubt it'd ever been used in Skyline. It was mainly added as a way of getting from that proprietary XML format to a more common/open format like mzXML/mzML.

The second error is you trying to use MGF data in Skyline. MGF doesn't really support MS1s so it's MS2 data that you converted to mzML so that Skyline would try to read it, but it still doesn't have MS1s. That error message could afford to be clearer. Something like "The current filter settings are looking for MS1 scans but the file only has MS2s." would have been helpful here.

Hope this helps!

fcsigloch responded:  2019-04-25

Hi Matt!

Thanks for the reply. Unfortunately, the data comes from a Bruker ion trap (amazon speed ETD), so even the .d will not help, I guess. Would conversion in to mzML help or is it just impossible to import these data?

Do you happen to know if there is any free software that can analyze this kind of data? MaxQuant will not help, I guess. What about OpenMS?

Kind regards,

fcsigloch responded:  2019-04-25

I found that MaxQuant should be able to process the data: Link.

matt.chambers42 responded:  2019-04-25

Msconvert can convert trap Bruker data (using CompassXtract library) to mzML, it's just Skyline that can't do that because it intentionally excludes that library. After converting to mzML then Skyline can read it. But what kind of acquisition method are you using? Is it designed for targeted quantitation?