Skyline document with cross-linked peptides

support
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

 
Nick Shulman responded:  2020-07-13
Daniela,

There is a new version of the Proxl xml converter for pLink which fixes this problem.
You can download it from here:
https://github.com/yeastrc/proxl-import-plink2/releases/

If you use this converter on your plink files, it will produce a proxl file which will work with the BiblioSpec in Skyline-Daily.

Thank you for testing the crosslinking feature in Skyline-Daily. Let us know if you run into any more problems or have other feedback.
-- Nick
 
danielacgranato responded:  2020-07-13
Dear Nick,
Thank you for the reply. We have tested the new version of the Proxl xml converter but we are still getting an error message, when trying to build BiblioSpec in Skyline Daily. I have copied the error message below. Please let me know if you would rather I attach the pLINK files as well. Thank you. Best, Daniela

Skyline-daily
---------------------------
ERROR: output06072020.proxl.xml(line 61): Missing required attribute 'linker_mass'.
ERROR:

Command-line: C:\Users\tatiz\AppData\Local\Apps\2.0\49BTDOGX.MMZ\O1B3EWR8.PN0\skyl..tion_e4141a2a22107248_0014.0001_03f97bc61082f05e\BlibBuild -s -A -H -o -c 0.95 -i 060702020 -S "C:\Users\tatiz\AppData\Local\Temp\tmp3C18.tmp" "C:\Users\tatiz\Downloads\060702020.redundant.blib"
Working directory: C:\plink_12_maio_2020
---------------------------
OK More Info
---------------------------
System.IO.IOException: ERROR: output06072020.proxl.xml(line 61): Missing required attribute 'linker_mass'.
ERROR:

Command-line: C:\Users\tatiz\AppData\Local\Apps\2.0\49BTDOGX.MMZ\O1B3EWR8.PN0\skyl..tion_e4141a2a22107248_0014.0001_03f97bc61082f05e\BlibBuild -s -A -H -o -c 0.95 -i 060702020 -S "C:\Users\tatiz\AppData\Local\Temp\tmp3C18.tmp" "C:\Users\tatiz\Downloads\060702020.redundant.blib"
Working directory: C:\plink_12_maio_2020
   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& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 156
---------------------------
 
Nick Shulman responded:  2020-07-13
I believe we have a fix for this linker_mass issue which will appear in the next Skyline-Daily.

If you would like to take a look at what is going to be in the next Skyline-Daily before then, you can download what we call the "Bleeding Edge" build.

To download the bleeding edge Skyline build, do the following steps:
1. Go to this URL:
https://teamcity.labkey.org/viewType.html?buildTypeId=bt209&branch_ProteoWizard=%3Cdefault%3E&tab=buildTypeStatusDiv
2. On the page that comes up, click "Log in as guest".
The page that comes up will have a list of recent builds that have happened. In the rightmost column is an icon that looks like a stack of papers. If you hover the mouse over that icon, a window appears that includes "SkylineTester.zip". Right-click on SkylineTester.zip and choose "Save Link As" and save that .zip file somewhere on your computer.
3. In Windows Explorer, right-click on the .zip file you downloaded, and choose "Properties". In the Properties dialog that comes up, click the checkbox that says "Unblock" and then push "OK". This step is usually necessary in order that the files that you extract in step 4 are able to run without error.
4. Extract all of the files from the .zip file.
5. Inside of the folder with the files that you extracted there will be a folder called "SkylineTester Files" which will contain "Skyline-Daily.exe". Run that Skyline-Daily.exe.

I hope this works for you.
Let me know if this does not work for you. There are other ways that I can send you a build of Skyline-Daily that will fix this BiblioSpec problem.
-- Nick
 
danielacgranato responded:  2020-07-16
Dear Nick,
Thank you very much for fixing this issue. I have used the new version of Skyline Daily but I´m still encountering some errors. I have attached the documents that I am using to build the BiblioSpec. Please let me know if you need anymore information. Best, Daniela

---------------------------
Skyline-daily
---------------------------
ERROR: output_basic.proxl.xml(line 51): Missing required attribute 'scan_file_name'.
ERROR:
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_d48b0c62650f389e\BlibBuild -s -A -H -o -c 0 -i pLINK -S "C:\Users\Daniela\AppData\Local\Temp\tmp911B.tmp" "C:\Users\Daniela\OneDrive\Documents\Lab_APL\1-Paper_Trx\crosslinked_peps_Skyline\zip\raw_files_MS2\pLINK.redundant.blib"
Working directory: C:\Users\Daniela\OneDrive\Documents\Lab_APL\1-Paper_Trx\crosslinked_peps_Skyline\all
---------------------------
OK More Info
---------------------------
System.IO.IOException: ERROR: output_basic.proxl.xml(line 51): Missing required attribute 'scan_file_name'.
ERROR:
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_d48b0c62650f389e\BlibBuild -s -A -H -o -c 0 -i pLINK -S "C:\Users\Daniela\AppData\Local\Temp\tmp911B.tmp" "C:\Users\Daniela\OneDrive\Documents\Lab_APL\1-Paper_Trx\crosslinked_peps_Skyline\zip\raw_files_MS2\pLINK.redundant.blib"
Working directory: C:\Users\Daniela\OneDrive\Documents\Lab_APL\1-Paper_Trx\crosslinked_peps_Skyline\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
---------------------------
 
Nick Shulman responded:  2020-07-16
Daniela,

Thank you for sending us your new .proxl.xml files.
Are you sure that the error that you are seeing is "Missing required attribute 'scan_file_name'"?
That is the error that you would get if you had used an older version of the plink to proxl converter. The .proxl.xml files that you attached look like they were created with a newer version.
The error that I get when I try to build a library from your .proxl.xml file is "ERROR: No spectra were found for the new library."

There are a number of things that Skyline and BiblioSpec are doing wrong here and I hope that we will be able to fix them soon.
-- Nick
 
Nick Shulman responded:  2020-07-17
Daniela,

We are working on fixing the bugs that prevent you from creating a .blib file.
One thing that we are a little confused about is the static cysteine modifications in the proxl.xml files that you have attached.
"basic_ss.proxl.xml" contains this line:
        <static_modification amino_acid="C" mass_change="57.0215"/>
and "complex_ss.proxl.xml" contains this line:
        <static_modification amino_acid="C" mass_change="-1.0073"/>

Neither of those is what we would expect to find in an experiment looking at disulfide bonds. Normally, I think, cysteine would have no static modification, and the crosslinker would have the chemical formula "-H2".

I just wanted to make sure that BiblioSpec is going to be interpreting the .proxl.xml files correctly, and that there are no bugs in our plink to proxl converter.
-- Nick