IM data in Skyline? | mnt | 2021-10-18 06:50 | |||||||||
Hello Skyline Lately i have been attempting to analyze som data from our TimsTof Pro2 with the PASEF engaged. The workflow i'm attempting to use is the following: Data is aquiered via our TimsTof Pro 2 with PASEF engaged, the .d files are converted both to .mgf and .mzML vi MSConvert. Here the "Combine ion mobility scans" is tjecked. The .mgf file are analyzed via xiSEARCH where a .ssl file is generated for Skyline. The .ssl file is placed in a folder with the .mzML files wherefrom it is opened in Skyline as part of building my library. However, this process (buildign the library) fails with the following error: --------------------------- Skyline --------------------------- ERROR: No spectra were found for the new library. Command-line: C:\Users\D42881\AppData\Local\Apps\2.0\QJTKV4CR.ROX\EEB2DNKN.1HP\skyl..tion_e4141a2a22107248_0015.0001_62a9d240a069a6b4\BlibBuild -s -A -H -o -c 0.95 -i TimsOnTest -K -S "C:\Users\D42881\AppData\Local\Temp\tmpDACB.tmp" "D:\MNT\Data\P035\Skyline\TimsOnTest.redundant.blib" Working directory: D:\MNT\Data\P035\Data\mzML --------------------------- OK More Info --------------------------- System.IO.IOException: ERROR: No spectra were found for the new library. Command-line: C:\Users\D42881\AppData\Local\Apps\2.0\QJTKV4CR.ROX\EEB2DNKN.1HP\skyl..tion_e4141a2a22107248_0015.0001_62a9d240a069a6b4\BlibBuild -s -A -H -o -c 0.95 -i TimsOnTest -K -S "C:\Users\D42881\AppData\Local\Temp\tmpDACB.tmp" "D:\MNT\Data\P035\Skyline\TimsOnTest.redundant.blib" Working directory: D:\MNT\Data\P035\Data\mzML at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 142 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157 --------------------------- The interesting thing is that this workflow works perfectly when the PASEF is not engaged. So, whatever this is, it has to do with the PASEF. |
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