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):
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Skyline
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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
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OK More Info
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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
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I attach to this post the msm.txt files and corresponding mqpar.xm.
please let me know if you need more information.