Problem Importing pep.xml File from PeaksX Search of Waters MSe Data

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Problem Importing pep.xml File from PeaksX Search of Waters MSe Data dwwilk02  2019-10-29
 
Hi,

I've gotten the error message listed below in Skyline 19.1.0.193 when I try to import a pep.xml file from a PeaksX search of waters MSe data. The MSe data was converted to mzML prior to the search in PeaksX. I attached the pep.xml file that was generated by PeaksX. Thanks for any suggestions. The error message is:

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Skyline
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ERROR: peptides.pep.xml(line 3463): [Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type
ERROR:

Command-line: C:\Users\dwwilk02.AD\AppData\Local\Apps\2.0\VLVOVZ8Y.QJE\9QMYDTGV.WT6\skyl..tion_e4141a2a22107248_0013.0001_f6e2bff174ff9e23\BlibBuild -s -A -H -o -c 0.95 -i CytokineQuanSkylineTemplateTest191029 -S "C:\Users\dwwilk02.AD\AppData\Local\Temp\tmp2B91.tmp" "C:\Users\dwwilk02.AD\Desktop\Temp Data\Cytokine Quantification\CytokineQuanSkylineTemplateTest191029.redundant.blib"
Working directory: C:\Users\dwwilk02.AD\Desktop\Synapt_MSe_Test_191001_PEAKS_91
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OK More Info
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System.IO.IOException: ERROR: peptides.pep.xml(line 3463): [Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type
ERROR:

Command-line: C:\Users\dwwilk02.AD\AppData\Local\Apps\2.0\VLVOVZ8Y.QJE\9QMYDTGV.WT6\skyl..tion_e4141a2a22107248_0013.0001_f6e2bff174ff9e23\BlibBuild -s -A -H -o -c 0.95 -i CytokineQuanSkylineTemplateTest191029 -S "C:\Users\dwwilk02.AD\AppData\Local\Temp\tmp2B91.tmp" "C:\Users\dwwilk02.AD\Desktop\Temp Data\Cytokine Quantification\CytokineQuanSkylineTemplateTest191029.redundant.blib"
Working directory: C:\Users\dwwilk02.AD\Desktop\Synapt_MSe_Test_191001_PEAKS_91
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_19_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 62
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in C:\proj\skyline_19_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 186
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 144
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Nick Shulman responded:  2019-10-29
I think it might be having trouble with trying to read the .mzXML file that is associated with the pepXML file.

Do you have a file there called "191018_SpikeMixHumanLight_01PeakPick.mzXML" or "191018_SpikeMixHumanLight_01PeakPick.mzML"?

I am a little confused because the error that you are getting says "mzXML" in it, but your pepXML file says "191018_SpikeMixHumanLight_01PeakPick.mzML".

BiblioSpec is trying to figure out which type of mass spectrometer that file came from (in order to know how to interpret the scan numbers) and it does not appear to come from any of the mass spectrometers we know about.

Can you send us that .mzML or .mzXML file? That file is probably too large to attach to a support request so you can upload it here:
https://skyline.ms/files.url

(If it's not too many files, it might help if you zipped up the whole folder "Synapt_MSe_Test_191001_PEAKS_91" and sent it to us in case there are other files in there that are needed to reproduce this error.)
-- Nick
 
dwwilk02 responded:  2019-10-29
Thanks Nick. I originally searched an mzML file in PeaksX, but it created an mzXML file when it exported the pep.xml file. I'll upload those files to the link you sent. I was able to import the mzML file into the Skyline document I created, but for the mzXML, I got the message:
 
At 3:48 PM:
Failed importing results file 'C:\Users\dwwilk02.AD\191018_SpikeMixHumanLight_01PeakPick.mzxml'.
[Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type
 
Thanks for any help,
Daniel
 
Nick Shulman responded:  2019-10-29
It sounds like the .mzXML files are in a format that we cannot handle.
The problem seems to be that BiblioSpec finds the .mzXML files instead of finding the .mzML files.

You should try deleting the .mzXML files, but make sure that that .mzML files are still somewhere that BiblioSpec will be able to find them (either in the same directory as the pepXML files, or one or two directories above that).
-- Nick