Hi Tim,
Do you mind posting the pepXML file that is giving you the problem? You can attach it here or upload it at https://skyline.ms/files.url

Thanks,
Kaipo

Hi Kaipo,

Thanks. Here's a pep.xml and an mzid, both of which give different errors. I really appreciate you taking a look at this.

Best,

Tim

Hi Kaipo,

Thanks. Here's a pep.xml and an mzid, both of which give different errors. I really appreciate you taking a look at this.

Best,

Tim

Having trouble with attaching the mzid, will skip it for now.

Tim

Hi Tim,
Sorry, I thought for sure we supported this workflow. In the current of version for Skyline, for Comet/Percolator we only support Percolator XML output with .ms2 spectra files (I believe that executing Crux with the --pout-output T option should generate this XML file). However I will add support for pepXML in this format from Crux/Percolator and it should be available in the next release of Skyline-daily.

Thanks,
Kaipo

Hi Kaipo,

Great to know!

Thank you kindly,

Tim

Hello Tim and Kaipo,

Sorry to bring back this thread but I believe it would be a related/same problem, are there any plans to support other kind of input/output combinations for the crux>comet>percolator workflow ?

Right now I am facing problems in several regards (would like to report the problem/ make a feature request),

1. The workflow outputs the .perc.xml (how it is looked for inside skyline) file with the extension .pout.xml (which should be "solvable" by a name change) .
2. The workflow automatically renames the files (when many) in the 'xml' outputs as indexes and assigns the file as "NA" in the percolator final output (which in turn makes skyline search for a file named target_0[.ms2|.cms2|.bms2|.pms2] or NA.[ms2 ...] respectively ).
   • The names of the indexes given can be found in the pipeline.log file.
3. Whenever using the percolator xml output, skyline looks for a .ms2|.cms2|.bms2|.pms2 raw file but whenever using the percolator.pep.xml it looks for a mzML|mzXML , which would be the supported input ?
4. Whenever attempting to use the comet output it returns the following error.

---------------------------
Skyline-daily
---------------------------
ERROR: comet.target.pep.xml(line 111): The .pep.xml file is not from one of the recognized sources
ERROR: 

---------------------------
OK More Info
---------------------------
System.IO.IOException: ERROR: comet.target.pep.xml(line 111): The .pep.xml file is not from one of the recognized sources
ERROR: 

   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 59
   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 171
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 137
---------------------------

where line 111 is:

 <spectrum_query spectrum="comet.00002.00002.3" start_scan="2" end_scan="2" precursor_neutral_mass="1000.703724" assumed_charge="3" index="1" retention_time_sec="1.3">

I would really appreciate if this fixes were possible or if documentation was available to make the workflow compatible.

Thank you very much for you attention and the amazing software !
Sebastian

ps: I would be willing to write a small tutorial once I figure out how to carry out the process or whenever it is implemented.

Hi Sebastian,

Can you upload examples of the "when many" workflow and the corresponding pipeline.log file you mention? Also an XML from the Comet workflow.

Thanks,
-Matt

Hello Matt,

Thank you for the quick response, I am attaching the full output of a reproducible example based on the tutorial on the crux website.
I am adding as well a small script to reproduce such example.

Kindest wishes,
Sebastian

Hello all,

I still cannot load spectral libraries from a Crux executed Comet search. I have the same exact problem as above. I know that one of the fixes some time ago was aimed at fixing this issue, but don't see the difference on my end. Can anyone provide any guidance on this please?

Thank you,

Tim

Are you using the latest Skyline-daily?

Yes.

Does your pepXML have 'search_engine="Comet"' in the <search_summary> element (should be first few lines of the file)? What version number do you see for Skyline -> Help -> About?

Using the current Skyline daily code I have no problem with the Comet pepXML from the crux-demo archive attached above. If you've got one that's still a problem I'd like to see it.

Now I've had a chance to look at the Percolator files too:

The perc.xml reader seems to depend on SQT files being present to read scan times from. Are those produced as part of this pipeline? Without them I don't think that reader is applicable (although it does have the filename association issues mentioned above and they could probably be fixed by looking at pipeline.log).

The percolator.target.pep.xml file is useless. Yes it has the basename set to NA, but the spectrum_query elements don't have indexes to map them back to files in pipeline.log. :(