mzid file contains unknown score type ERROR Shawn Rice  2019-06-12 11:18
 

Greetings,

I was trying to import an mzid file from a ProteinPilot search into SkylineDaily v19.0.9.149 and received and unknown score type ERROR. Do you have any suggestions to get this to work. The complete error message is below.

Thanks,
Shawn

Skyline-daily

ERROR: .mzid file contains an unsupported score type

Command-line: C:\Users\srice\AppData\Local\Apps\2.0\1HWJB6KR.0MJ\D4N33RE7.E7A\skyl..tion_e4141a2a22107248_0013.0000_8870d1d2982721de\BlibBuild -s -A -H -o -c 0 -i proteinpilot -S "C:\Users\srice\AppData\Local\Temp\tmp513.tmp" "M:\06-2019\proteinpilot.redundant.blib"
Working directory: C:\Users\srice\Downloads

OK More Info

System.IO.IOException: ERROR: .mzid file contains an unsupported score type

Command-line: C:\Users\srice\AppData\Local\Apps\2.0\1HWJB6KR.0MJ\D4N33RE7.E7A\skyl..tion_e4141a2a22107248_0013.0000_8870d1d2982721de\BlibBuild -s -A -H -o -c 0 -i proteinpilot -S "C:\Users\srice\AppData\Local\Temp\tmp513.tmp" "M:\06-2019\proteinpilot.redundant.blib"
Working directory: C:\Users\srice\Downloads
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\pwiz_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\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 186
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 144
 
 
Matt Chambers responded:  2019-06-13 09:48

Hi Shawn,

We currently only support importing ProteinPilot XML (created by the group2xml tool). But if you upload us one of the mzIdentMLs I'll try to add support for that route.

Thanks,
-Matt
 
Shawn Rice responded:  2019-06-13 10:43

Matt,

Where do you get the group2xml tool?

I attached a file for you to take a look at.

Thanks,
Shawn
 
Matt Chambers responded:  2019-06-13 10:49

I don't see an attachment?
 
Shawn Rice responded:  2019-06-13 11:35

I'll try it again.
 
Matt Chambers responded:  2019-06-13 12:02

Yes, I can add support for this easily. In order to create a test can you send 2 of the mzML/mzXML/MGF you searched that produced this file? You may have to convert them from WIFFs first. (I will be trimming down and deidentifying the files to make the test data small). I notice this file has spectra from 6 WIFFs in it, but the spectraData refs all say SD_1. The list of spectraData elements does have SD_1 through SD_6. So this appears to be a bug in their mzIdentML writer. Fortunately their SpectrumIDentificationResult elements have a file=x key so I can use that to hack in support for it.

If the file are really large you may need to use the file upload area (https://skyline.ms/project/home/support/file sharing/start.view?), or I can give you some commands to trim the file down on your end.
 
Shawn Rice responded:  2019-06-13 13:02

Matt,
The files are uploading may take awhile (1.6 G each). The files are sjr04302019_1.mzML and sjr04302019_2.mzML.

Thanks,
Shawn
 
Brendan MacLean responded:  2019-06-13 13:42

Skyline looks in the Windows registry for a key that it expects ProteinPilot to write if it has been installed:

SOFTWARE\Classes\groFile\shell\open\command

It gets the path of this command and then looks for either 1) GroupFileExtractor.exe or 2) group2xml.exe

If it finds either, Skyline itself will use one of these EXE files to convert your .group file to .group.xml

So, if you are using ProteinPilot and you have it installed on the same machine as Skyline, you should be able to have Skyline build libraries from .group file results directly. If you have ProteinPilot installed elsewhere, you should be able to use this same method to find one of the conversion EXEs and convert from .group to .group.xml, which Skyline knows how to deal with without needing any further conversion.

But, also, we are always open to supporting new mzIdentML as long as we can get useful examples of it.

Thanks for helping Matt get the necessary files to allow him to add support for this into the library builder.

--Brendan
 
Matt Chambers responded:  2019-06-14 13:21

It's fixed now. You can either wait for the next Skyline.daily or update your BiblioSpec executables by downloading new ones from: http://teamcity.labkey.org/repository/download/bt209/765983:id/BiblioSpec.zip?guest=1

Where to put put the new executables depends on which Skyline you have installed (admin install to Program Files or clickonce)