pepxml-mzXML import from PEAKS no longer works

support
pepxml-mzXML import from PEAKS no longer works dkueltz  2021-12-08
 
Hi,
My lab has used Skyline for many years to import pepxml (and corresponding mzXML) generated by PEAKS and it always worked well until very recently when I get the error pasted below. Importing pepxml + mzML from MSfragger still works well. I wonder whether the pepxml + mzXML import function in Skyline has changed? Could you please look at the error below and let me know how to fix it such that my lab can continue to use our pipeline of generating spec libs from PEAKS DDA data?
Thanks much,
Dietmar

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Skyline
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ERROR: peptides.pep.xml(line 22656): [Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type
ERROR:

Command-line: C:\Users\dkueltz\AppData\Local\Apps\2.0\8JR1V559.JCC\KOCQGHPK.M36\skyl..tion_e4141a2a22107248_0015.0001_62a9d240a069a6b4\BlibBuild -s -A -H -o -c 0.95 -i test6 -S "C:\Users\dkueltz\AppData\Local\Temp\tmpB6D.tmp" "D:\Spectral-Libraries\test6.redundant.blib"
Working directory: F:\EAM0021-24_Oremo_V8-AmBic_60min\PEAKS-to-Skyline\PEAKS10Pro_Oremo_V8-AmBic_Histones_PEAKS PTM_35
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OK More Info
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System.IO.IOException: ERROR: peptides.pep.xml(line 22656): [Serializer_mzXML::translateSourceFileTypeToNativeIdFormat] unknown file type
ERROR:

Command-line: C:\Users\dkueltz\AppData\Local\Apps\2.0\8JR1V559.JCC\KOCQGHPK.M36\skyl..tion_e4141a2a22107248_0015.0001_62a9d240a069a6b4\BlibBuild -s -A -H -o -c 0.95 -i test6 -S "C:\Users\dkueltz\AppData\Local\Temp\tmpB6D.tmp" "D:\Spectral-Libraries\test6.redundant.blib"
Working directory: F:\EAM0021-24_Oremo_V8-AmBic_60min\PEAKS-to-Skyline\PEAKS10Pro_Oremo_V8-AmBic_Histones_PEAKS PTM_35
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 142
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157
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Nick Shulman responded:  2021-12-08
I can't tell what is going wrong from that error message. I suspect there is something wrong with the .mzXML file and if you were to try to extract chromatograms from it in Skyline or look at it in ProteoWizard SeeMS.exe you would see the same error.

Can you send us your pep.xml file and that .mzXML file?

You can upload them here:
https://skyline.ms/files.url
--Nick
 
dkueltz responded:  2021-12-08
Hi Nick,

Thanks for taking a look at this. I have uploaded a zip folder containing the pepxml and corresponding mzXML to the online link you had provided. I find this error strange since it always worked well before with a lot of different PEAKS exported files. Hopefully, finding the cause of the error is straightforward.

I appreciate your help,
Dietmar
 
Nick Shulman responded:  2021-12-08
The "unknown file type" that ProteoWizard is complaining about is "mzML".
It looks like ProteoWizard needs to know what type of file the .mzXML file originally came from, and "mzML" is not specific enough.

One thing that might work would be to delete the .mzXML file, and make it so ProteoWizard finds the .mzML file instead when it is looking for the raw file that goes with the pepXML file.

Are you sure that this used to work mzXML files in the past? If you send us one of your older mzXML files, I could probably figure out why it used to work. My guess is that there is something in the older mzXML files which tells ProteoWizard what the original raw file type was.

I am not the expert on mzXML files in ProteoWizard. Someone else on this support board might be able to tell you what is actually going on and how and whether this is supposed to work.
-- Nick
 
dkueltz responded:  2021-12-08
Hi Nick,

That explanation made perfect sense. I used to load bruker.d raw data into PEAKS and they were probably converted to mzXML. Now I am using mzML files generated using MSConvert (from bruker.d) for loading into PEAKS since I need to convert to mzML for MSfragger anyway. To minimize the amount of raw data that needs to be submitted to public repositories I am standardizing all raw data to mzML.

After copying the corresponding mzML file into the folder that contains the pepxml and mzXML files it worked like a charm.

Thanks again for your help - much appreciated!
Dietmar