Error building spectral libraries from Comet/percolator output

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Error building spectral libraries from Comet/percolator output timothy acker  2018-05-23
 

Hi All,

I hope this message finds you well. I am having a recurring problem building spectral libraries or importing search results from Comet/percolator output.

In peptide settings when I try to create a spectral library or import results, I am given an error informing me that the pep.xml file is not from one of the recognized file format and it references the first line in the search results within the pep.xml file. I am running comet from the crux interface in Cygwin.

crux v 3.1.windows.amd64, percolator v 3.02.0, Skyline v 4.1.0.11796, Comet version "2017.01 rev. 4"

I cannot find another example in the support forums.

Thank you,

Tim

 
 
Kaipo responded:  2018-05-24

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

 
timothy acker responded:  2018-05-25

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

 
timothy acker responded:  2018-05-25

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

 
timothy acker responded:  2018-05-25
 
timothy acker responded:  2018-05-25

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

Tim

 
Kaipo responded:  2018-05-25

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

 
timothy acker responded:  2018-05-25

Hi Kaipo,

Great to know!

Thank you kindly,

Tim

 
jpaezpae responded:  2018-10-04

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.

 
matt.chambers42 responded:  2018-10-05

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

 
jpaezpae responded:  2018-10-05

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