Dear Skyline Team!
My group is working on a variant of isoTOP-ABPP (MS1 quantification) to study the target engagement of covalent inhibitors using chemoproteomics. I have now tested Skyline for Quantification of MSFragger search results and it works great. We have to use a workaround that uses selenocysteine as placeholder for a modified residue, which we have established before for MaxQuant searches/quantification (https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201912075), but than it works out very well. In principle, this strategy should also be transferable to quantify MaxQuant search results in Skyline. Nevertheless, when I want to load the MaxQuant data with a modification (IA heavy isoDTB U2) on selenocysteine into Skyline, I get the following error message (screenshot attached):
System.IO.IOException: ERROR: No matching mod for IA heavy isoDTB U2 in sequence AAANIGLEPEEVAIITGIGU(IA heavy isoDTB U2)SGR (line 2). Make sure you have provided the correct modifications[.local].xml file.
Command-line: C:\Users\AKHacker3\AppData\Local\Apps\2.0\1AYPALAY.4DC\R6XMQK52.Z7A\skyl..tion_e4141a2a22107248_0015.0001_e8c6979bec685b9e\BlibBuild -s -A -H -o -c 0 -i 181207_P05_P06 -S "C:\Users\AKHacker3\AppData\Local\Temp\tmpEE5D.tmp" "C:\current_analysis\SMH\013_181207_P05_P06\MQ_2_0_3_0_mod_U_CAM_var2\skyline2\181207_P05_P06.redundant.blib"
Working directory: C:\current_analysis\SMH\013_181207_P05_P06\MQ_2_0_3_0_mod_U_CAM_var2\skyline2
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\pwiz_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\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 157
The IA heavy isoDTB U2 modification on U is defined in the modifications.local.xml (attached), which is put into the same folder. I think, this might be related to the U creating a problem.
Might this be something someone on your end could look into? I have uploaded the full data, I wanted to use, here:
This data set also has screenshots of the modifications that we wanted to use. The same setup works for analyzing MSFragger data in Skyline and gives, as said, really nice data.
It would be great, if you could give some input.