cannot find and use modifications present in unimod

support
cannot find and use modifications present in unimod pavel shliaha  2022-03-24
 
Unimod has shTMT modification under 2015accession. I cannot find it in the structural modification list and using V(unimod: 2015)LHSGSR returns an error. Is it possible to import this modification into my skyline

---------------------------
Skyline
---------------------------
Unrecognized Unimod id 2015 in modified peptide sequence V(unimod:2015)LHSGSR (amino acid 1, V(unimod:2015)).
---------------------------
OK More Info
---------------------------
System.FormatException: Unrecognized Unimod id 2015 in modified peptide sequence V(unimod:2015)LHSGSR (amino acid 1, V(unimod:2015)).
   at pwiz.Skyline.Model.ModificationMatcher.ThrowUnimodException(String seq, Int32 uniModId, Int32 indexAA, Int32 indexBracket, Int32 indexClose) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 396
   at pwiz.Skyline.Model.ModificationMatcher.SimplifyUnimodSequence(String seq) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 364
   at pwiz.Skyline.Model.ModificationMatcher.IsMatch(Target target, PeptideDocNode nodePep, TransitionGroupDocNode& nodeGroup) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 454
   at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(Target target, Peptide peptide, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 644
   at pwiz.Skyline.Model.ModificationMatcher.MoveNextSequence() in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 78
   at pwiz.Skyline.Model.AbstractModificationMatcher.InitMatcherSettings(SrmSettings settings, MappedList`2 defSetStatic, MappedList`2 defSetHeavy) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 81
   at pwiz.Skyline.Model.ModificationMatcher.CreateMatches(SrmSettings settings, IEnumerable`1 sequences, MappedList`2 defSetStatic, MappedList`2 defSetHeavy, IProgressMonitor progressMonitor, IProgressStatus status) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 61
   at pwiz.Skyline.SkylineWindow.ImportFasta(TextReader reader, Int64 lineCount, Boolean peptideList, String description, ImportFastaInfo importInfo) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1629
---------------------------
 
 
Nick Shulman responded:  2022-03-24
It looks like you are doing:
File > Import > FASTA
and Skyline is complaining about something related to modifications.

I am not familiar with FASTA files having modifications in them, but if you send us your Skyline document and FASTA file we will probably be able to figure out what is going wrong.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.

If that .zip file and your FASTA file are less than 50MB you can attach them to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick