Skyline document with cross-linked peptides

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Skyline document with cross-linked peptides danielacgranato  2020-06-27
 

Sorry, I forgot to attach the documents in the prior message (pLINK output and prox.xml converted). Thank you very much. Best, Daniela

 
 
Nick Shulman responded:  2020-06-27
Thank you for reporting this problem.

I am going to email a few people and figure out how this feature is supposed to work with plink files.
--Nick
 
Brendan MacLean responded:  2020-06-27
Somehow we lost the original message which came through in email before this one. It is helpful to understand what this post is about. So, I am posting it again here.

Dear,
I am trying to create, in Skyline-Daily, a spectral library (.blib) from .proxl files. To do so I converted the pLINK output files (attached) in proxl.xml files (attached). For some reason when I add them to Skyline I get the following error message bellow. Could you please help to troubleshoot this problem. Thank you veru much. Best, Daniela
Skyline-daily
ERROR: output_complex.proxl.xml(line 51): Missing required attribute 'scan_file_name'.
ERROR:

Command-line: C:\Users\Daniela\AppData\Local\Apps\2.0\3LM72267.TR1\62PY4P4B.7E3\skyl..tion_e4141a2a22107248_0014.0001_03f97bc61082f05e\BlibBuild -s -A -H -o -c 0.95 -i tester -S "C:\Users\Daniela\AppData\Local\Temp\tmpBF5D.tmp" "C:\Users\Daniela\OneDrive\Desktop\tester.redundant.blib"
Working directory: C:\Users\Daniela\OneDrive\Documents\Lab_APL\1-Paper_Trx\all
OK More Info
System.IO.IOException: ERROR: output_complex.proxl.xml(line 51): Missing required attribute 'scan_file_name'.
ERROR:

Command-line: C:\Users\Daniela\AppData\Local\Apps\2.0\3LM72267.TR1\62PY4P4B.7E3\skyl..tion_e4141a2a22107248_0014.0001_03f97bc61082f05e\BlibBuild -s -A -H -o -c 0.95 -i tester -S "C:\Users\Daniela\AppData\Local\Temp\tmpBF5D.tmp" "C:\Users\Daniela\OneDrive\Desktop\tester.redundant.blib"
Working directory: C:\Users\Daniela\OneDrive\Documents\Lab_APL\1-Paper_Trx\all
em pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) na C:\proj\pwiz_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:linha 62
em pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) na C:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:linha 201
em pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) na C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:linha 156
 
Brendan MacLean responded:  2020-06-27

Hi Daniela,
We are not very familiar with this software, which seems to have its main page here:

http://pfind.ict.ac.cn/software/pLink/index.html

When we build a spectral library from search results, we generally want the search engine to provide:

  1. Spectra
  2. Spectrum source files
  3. Spectrum acquisition times / retention times

We are finding it a bit challenging to find this in the pLink files you have provided in the ZIP file plink_12_maio_2020.zip which you provided. Nor do they appear to be in the proxl.xml file.

Where did you get the proxl XML converter from? Is it provided by the pLink team or the Proxl project? Have you used this XML with Proxl itself? If so, have you noticed any issues with Proxl?

There is a pLink demo on Proxl:

https://www.yeastrc.org/proxl_public/peptide.do?projectSearchId=20

I am able to browse all the way to viewing spectra by clicking on a peptide and then clicking on a "View Spectrum". So, somehow Proxl seems to have gotten the spectra for these results and I see retention times reported.

However, I don't see any way of getting this information from the proxl.xml you have provided. Can you see it in there? Can you perhaps help us learn more from the providers of the tools you are using?

Thanks for your interest in testing our new cross-linked peptide support. With a little help we hope to get you past this quickly.

--Brendan