issue when importing peptide search from a MaxQuant msms.txt file marie locard-paulet21061  2020-05-01 06:59
 

Hello, I am trying to import the results of a DDA search from MaxQuant (1.6.14) for generating a library in Skyline (for DIA data analysis).
I work with Skyline (64-bit) 20.1.0.76 (0d62150d0). My samples do not contain iRTs, and kept all default parameters for the "import peptide search".

Here is the error message that I get (copied and pasted from Skyline):

---------------------------
Skyline
---------------------------
ERROR: No spectra were found for the new library.

Command-line: C:\Users\malopa\AppData\Local\Apps\2.0\5ZNXQLMA.P6A\TRMG87OZ.R8T\skyl..tion_e4141a2a22107248_0014.0001_72292abfbc2fefb5\BlibBuild -s -A -H -o -c 0.95 -i MQDDALib_MC1_Carba -S "C:\Users\malopa\AppData\Local\Temp\2\tmp3F62.tmp" "C:\data\Skyline\MQDDALib_MC1_Carba\MQDDALib_MC1_Carba.redundant.blib"
Working directory: C:\data\MQ\HeLA_21min_Library\MQDDA_MC1_Carba\combined\txt
---------------------------
OK More Info
---------------------------
System.IO.IOException: ERROR: No spectra were found for the new library.

Command-line: C:\Users\malopa\AppData\Local\Apps\2.0\5ZNXQLMA.P6A\TRMG87OZ.R8T\skyl..tion_e4141a2a22107248_0014.0001_72292abfbc2fefb5\BlibBuild -s -A -H -o -c 0.95 -i MQDDALib_MC1_Carba -S "C:\Users\malopa\AppData\Local\Temp\2\tmp3F62.tmp" "C:\data\Skyline\MQDDALib_MC1_Carba\MQDDALib_MC1_Carba.redundant.blib"
Working directory: C:\data\MQ\HeLA_21min_Library\MQDDA_MC1_Carba\combined\txt
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_1_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\skyline_20_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 160
---------------------------

I attach to this post the msm.txt files and corresponding mqpar.xm.
please let me know if you need more information.
 
 
Nick Shulman responded:  2020-05-01 12:13
I do not see any files attached to this support request. This sometimes happens if the files you are trying to attach are too large (greater than 50MB).

You can upload your files here:
https://skyline.ms/files.url

-- Nick
 
marie locard-paulet21061 responded:  2020-05-02 03:34
Thanks Nick,

I have uploaded the zipped msms.txt. Let me know if you need anything more.

bests,
Marie.
 
Nick Shulman responded:  2020-05-02 13:27
Can you send me your mqpar.xml file? BiblioSpec won't let me try to build a library without it.
-- Nick
 
marie locard-paulet21061 responded:  2020-05-03 12:33
Hi,

sorry I thought it was sent with the first post.
It is uploaded now.

Thanks for your help,
Marie.
 
Nick Shulman responded:  2020-05-03 14:41
Thank you for sending us those files.

This is a bug in our code for reading MaxQuant data files.
There are two columns that might appear in a "msms.txt" files which are supposed to be treated as optional: "Labeling State" and "Evidence ID".
However, because of a mistake in the way that we wrote the code, at least one of those columns needs to be there, otherwise BiblioSpec fails to correctly read any of the data in the msms.txt file.

I will try to fix this in the next update of Skyline-Daily.

-- Nick