Hi,
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.