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Bibliospec not recognize modification from PLGS file

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Bibliospec not recognize modification from PLGS file jcaceresvergara  2022-12-02
 
I'm trying to create a library from a peptide search made using PLGS. I get the error at the end. It does not appear to understand the modification I set, I try to change the final_fragment.csv file or add the modification to my skyline file but nothing seems to work. can you help me with this?

The modification should be a loss of' -2HS' variable on cysteine. I'm attaching my final_fragment.csv file.

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Skyline-daily
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ERROR: The modification 'Dehydroalanine+C(4)' on line 1429 is not recognized. Supported modifications include: "12C d0", "13C", "13C N15", "13C d9", "1H d0", "2H d8", "Acetyl", "Amidation", "Biotin", "C-Mannosyl", "Carbamidomethyl", "Carbamyl", "Carboxymethyl", "DUPLEX_TANDEM_MASS_TAG126", "DUPLEX_TANDEM_MASS_TAG127", "Deamidation", "Dehydration", "Dimethyl", "Farnesyl", "Flavin-adenine", "Formyl", "Gamma-carboxyglutamic", "Geranyl-geranyl", "Glycation", "Hydroxyl", "ICAT-C", "ICAT-C13C(9)", "ICAT-D", "ICAT-D 2H(8)", "ICAT-G", "ICAT-G 2H(8)", "ICAT-H", "ICAT-H13(6)", "Isobaric 114", "Isobaric 115", "Isobaric 116", "Isobaric 117", "Isobaric 8plex 113", "Isobaric 8plex 114", "Isobaric 8plex 115", "Isobaric 8plex 116", "Isobaric 8plex 117", "Isobaric 8plex 118", "Isobaric 8plex 119", "Isobaric 8plex 121", "Lipoyl", "Methyl", "Myristoyl", "N-Glycosylation", "NATIVE_TANDEM_MASS_TAG126", "NATIVE_TANDEM_MASS_TAG127", "NIPCAM", "O-GlcNAc", "O-Glycosylation", "O18", "O18 label at both C-terminal oxygens", "Oxidation", "Palmitoyl", "Phosphopantetheine", "Phosphoryl", "Propionamide", "Pyridoxal", "Pyrrolidone", "S-pyridylethyl", "SILAC 13C(1) 2H3", "SILAC 13C(3)", "SILAC 13C(3) 15N(1)", "SILAC 13C(4) 15N(1)", "SILAC 13C(5)", "SILAC 13C(6)", "SILAC 13C(6) 15N(2)", "SILAC 13C(6) 15N(4)", "SILAC 13C(8) 15N(2)", "SILAC 13C(9)", "SILAC 13C(9) 15N(1)", "SILAC 15N(2) 2H(9)", "SILAC 15N(4)", "SIXPLEX_TANDEM_MASS_TAG126", "SIXPLEX_TANDEM_MASS_TAG127", "SIXPLEX_TANDEM_MASS_TAG128", "SIXPLEX_TANDEM_MASS_TAG129", "SIXPLEX_TANDEM_MASS_TAG130", "SIXPLEX_TANDEM_MASS_TAG131", "SMA", "Sulfo", "Trimethyl".
ERROR: reading file 20221122 C418U_iRT MSE JC_LC-05_IA_final_fragment.csv

Command-line: C:\Users\jcaceresvergara\AppData\Local\Apps\2.0\T0VY925W.HAY\GJ5BNRYZ.4Y7\skyl..tion_e4141a2a22107248_0016.0002_c984fd7cba69179e\BlibBuild -s -A -H -o -i lib -S "C:\Users\jcaceresvergara\AppData\Local\Temp\tmp6856.tmp" "D:\lib.redundant.blib"
Working directory: C:\Users\jcaceresvergara\Downloads\PLGS Search Results\PLGS Search Results\Trypsin\20221122 C418U_iRT MSE JC_LC-05_20221202133552
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OK More Info
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System.IO.IOException: ERROR: The modification 'Dehydroalanine+C(4)' on line 1429 is not recognized. Supported modifications include: "12C d0", "13C", "13C N15", "13C d9", "1H d0", "2H d8", "Acetyl", "Amidation", "Biotin", "C-Mannosyl", "Carbamidomethyl", "Carbamyl", "Carboxymethyl", "DUPLEX_TANDEM_MASS_TAG126", "DUPLEX_TANDEM_MASS_TAG127", "Deamidation", "Dehydration", "Dimethyl", "Farnesyl", "Flavin-adenine", "Formyl", "Gamma-carboxyglutamic", "Geranyl-geranyl", "Glycation", "Hydroxyl", "ICAT-C", "ICAT-C13C(9)", "ICAT-D", "ICAT-D 2H(8)", "ICAT-G", "ICAT-G 2H(8)", "ICAT-H", "ICAT-H13(6)", "Isobaric 114", "Isobaric 115", "Isobaric 116", "Isobaric 117", "Isobaric 8plex 113", "Isobaric 8plex 114", "Isobaric 8plex 115", "Isobaric 8plex 116", "Isobaric 8plex 117", "Isobaric 8plex 118", "Isobaric 8plex 119", "Isobaric 8plex 121", "Lipoyl", "Methyl", "Myristoyl", "N-Glycosylation", "NATIVE_TANDEM_MASS_TAG126", "NATIVE_TANDEM_MASS_TAG127", "NIPCAM", "O-GlcNAc", "O-Glycosylation", "O18", "O18 label at both C-terminal oxygens", "Oxidation", "Palmitoyl", "Phosphopantetheine", "Phosphoryl", "Propionamide", "Pyridoxal", "Pyrrolidone", "S-pyridylethyl", "SILAC 13C(1) 2H3", "SILAC 13C(3)", "SILAC 13C(3) 15N(1)", "SILAC 13C(4) 15N(1)", "SILAC 13C(5)", "SILAC 13C(6)", "SILAC 13C(6) 15N(2)", "SILAC 13C(6) 15N(4)", "SILAC 13C(8) 15N(2)", "SILAC 13C(9)", "SILAC 13C(9) 15N(1)", "SILAC 15N(2) 2H(9)", "SILAC 15N(4)", "SIXPLEX_TANDEM_MASS_TAG126", "SIXPLEX_TANDEM_MASS_TAG127", "SIXPLEX_TANDEM_MASS_TAG128", "SIXPLEX_TANDEM_MASS_TAG129", "SIXPLEX_TANDEM_MASS_TAG130", "SIXPLEX_TANDEM_MASS_TAG131", "SMA", "Sulfo", "Trimethyl".
ERROR: reading file 20221122 C418U_iRT MSE JC_LC-05_IA_final_fragment.csv

Command-line: C:\Users\jcaceresvergara\AppData\Local\Apps\2.0\T0VY925W.HAY\GJ5BNRYZ.4Y7\skyl..tion_e4141a2a22107248_0016.0002_c984fd7cba69179e\BlibBuild -s -A -H -o -i lib -S "C:\Users\jcaceresvergara\AppData\Local\Temp\tmp6856.tmp" "D:\lib.redundant.blib"
Working directory: C:\Users\jcaceresvergara\Downloads\PLGS Search Results\PLGS Search Results\Trypsin\20221122 C418U_iRT MSE JC_LC-05_20221202133552
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\pwiz\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 161
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 412
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161
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Nick Shulman responded:  2022-12-02
For these final_fragment.csv files, BiblioSpec has a hard-coded list of modifications that it understands.
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_tools/BiblioSpec/src/WatersMseReader.cpp#L60

The last time that we updated that list was in 2018 when a Waters employee sent us a file called "mod_list.txt" which they got from the "ProteinLynx GlobalSERVER folder environment".
I am thinking that maybe ProteinLynx GlobalServer is software that you might have installed on your computer, and if you do, there might be a file in there called "mod_list.txt" which is newer than the file we used from 2018.
If you do have a file called "mod_list.txt" on your computer, could you send it to us? I will then update BiblioSpec to support whatever modifications have been added in the last four years.
(If not, I'll ask Waters if they can send us a newer list of modifications)
-- Nick
 
jcaceresvergara responded:  2022-12-05
Hi Nick,

Thanks for the answer. I'm attaching the file, however this file will change depending on the user defined modifications (is installation dependent, not a general file).

I'm looking for several modifications and will probably add more over time so I'm not sure if it will be optimal to send this file to you every time. The file WatersMseReader.cpp looks straight forward to modify, but I cannot find it on my skyline installation. do you think I can edit it myself?

thanks a lot.
Juan Carlos.
 
Nick Shulman responded:  2022-12-05
No, editing "WatersMseReader.cpp" would not be straightforward. You would also need to recompile BlibBuild.exe.

I will ask around and see whether we can implement something where you could either tell BiblioSpec where to find mod_list.txt or copy it somewhere that BiblioSpec might be able to find it.
-- Nick
 
jcaceresvergara responded:  2022-12-08
oh ok.

Thanks a lot. please keep me posted.

Juan Carlos.
 
jcaceresvergara responded:  2023-02-28
Hi Nick,

I just wanted to follow up on this thread, do you know if the WatersMseReader.cpp file has been updated? or if you had implemented any way to tell BiblioSpec to read the mod_list file.

thanks a lot
I appreciate the help.

Juan Carlos.
 
Nick Shulman responded:  2023-02-28
I will forward you the discussion that we started back in December.
I think the plan was that the user would have to export the method as an XML file and put that file in the same folder as the "...final_fragment.csv" file. BiblioSpec would know to check to see if such a file was there. Then we got stuck on deciding things such as what that XML file should be named.
-- Nick