histone quantification

histone quantification mariette matondo  2020-07-22

I like to do some quantification of modified peptides with the Skyline software.
For identification I use the MaxQuant software v1.6
To quantify my data, I import the msms.txt from the MaxQuant search into Skyline I also paste the modification.local.xml file from MQ.
But I cannot import my peptides
in attached files the msms files and modification.local. xml file

Could you please help me

Many thanks,

Brian Pratt responded:  2020-07-22

Hi Mariette,

Perhaps you could provide some details on precisely what steps you took, and the results and/or errors you observed. Screen shots are helpful.

Thanks for using the Skyline support board!

Brian Pratt

mariette matondo responded:  2020-07-22

thanks Brian

here is the sreen shot

matt.chambers42 responded:  2020-07-22

Hi Mariette, can you share the mqpar.xml as well? Thanks.

mariette matondo responded:  2020-07-22

here is the file


mariette matondo responded:  2020-07-23

did you check my mqpar file?



mariette matondo responded:  2020-07-23

here is the error message:

System.IO.IOException: ERROR: No matching mod for tr in sequence (ac)AEIEHAK(tr)AQR (line 11). Make sure you have provided the correct modifications[.local].xml file.

Command-line: C:\Users\User_MM\AppData\Local\Apps\2.0\40E9NE9A.31E\6ZCRXR1Z.84W\skyl..tion_e4141a2a22107248_0014.0001_a618d1d4217289b5\BlibBuild -s -A -H -o -c 0.95 -i library -S "C:\Users\User_MM\AppData\Local\Temp\tmp6291.tmp" "X:\Projets\Bon\20200309_IP_Bon\skyline\library.redundant.blib"
Working directory: X:\Projets\Bon\20200309_IP_Bon\MQ_Output\20200716_Propionylation_variable_1_18\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

matt.chambers42 responded:  2020-07-23

OK I see what's happening. It's looking for the mod named "Trimethyl (KR)" but the mod in the default modifications.xml (distributed with BiblioSpec) is "Trimethyl (K)". Did you change the specificity of the mod in your modifications.xml? I see the default Dimethyl is (KR).

Mike MacCoss responded:  2020-07-23

I don't believe it is possible to have a trimethyl R. You can have both symmetric and asymmetric dimethyl-arginine but not trimethyl-arginine. It is possible to have trimethyl-lysine.