Modifications on Selenocysteine in MaxQuant data for Skyline

Modifications on Selenocysteine in MaxQuant data for Skyline s m hacker  2021-11-09

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 (, 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.

Nick Shulman responded:  2021-11-09
BiblioSpec is telling me that it also needs the file "mqpar.xml". Can you send give us that file too? I did not see that file at the link you provided.
-- Nick
s m hacker responded:  2021-11-09
Thank you for looking into this. I actually did not provide this file so far. Just putting it in the same folder has not helped on my end, sadly. The mqpar.xml is now attached to this post.
Nick Shulman responded:  2021-11-09
This problem has been reported a few times before:

There is a short list of elements which BiblioSpec understands when reading modifications from MaxQuant search results and Selenium is not in that list.

I will ask around again and see if someone can fix this.
-- Nick
s m hacker responded:  2021-11-09
Thanks so much. We might actually get around this by using O as the placeholder instead of U. That way we do not need to use selenium in the placeholder modification. Will try this tomorrow and give an update.
Nick Shulman responded:  2021-11-09
BiblioSpec is not having any trouble with the "U" amino acid that the modification applies to.

The problem is with the chemical formula of the modification:
C(24) Cx(4) H(46) N(8) Nx(2) O(6) S(1) Se(-1)

When BiblioSpec is reading MaxQuant search results, it does not know what to do with "Se". Many years ago we copied the list of elements and their masses from the MaxQuant source code, and we have not updated that list since then.
-- Nick
s m hacker responded:  2021-11-09
That makes sense. Nevertheless, we only need the S(1) Se (-1) part of the modification to computationally transfer the U that we use as a placeholder back to the C that is actually there in the proteome. So, if we instead use O as the placeholder, we will need a different modification for correction to transfer O to C, but this correction will not require a Se in that modification. So, I think it should work. I hope this makes sense.
s m hacker responded:  2021-11-10
A quick update: I have run it with O instead of U as the placeholder and, therefore, no selenium in the modification and now it works very well. Thanks so much for the help.
matt.chambers42 responded:  2021-12-03
All MaxQuant elements (like Se) will be supported in the next Skyline release and next Skyline-daily. Thanks for your patience!
s m hacker responded:  2021-12-03
Thank you so much. Looking forward to exploring this.