In order for me to reproduce this problem that you are running into, I would need some more files in addition to the .tsv.speclib that you attached.
I am not sure exactly which file(s) I would need.
One of the files that I need is some sort of report file whose name ends in .tsv.
It might be easiest if you could send me all of the files that are in the same folder as "Swissprot_HSapiens-BSA_lib.tsv.speclib".
You could package everything up into a .zip file and upload it here:
https://skyline.ms/files.url

I might be able to figure out what is going on if I could see the rest of that error message.
All Skyline message boxes have a Copy button in the lower left corner which will copy the text of the message plus the additional information that you would see if you press the "More Info" button.
It would be helpful if you could also send me that text.

-- Nick

Dear Nick,

Thx for the reply. Here the error msg:

---------------------------
Skyline
---------------------------
ERROR: unable to handle mod in library entry: AAAHHYGAQC(Unimod:4)DK3
ERROR: reading file Swissprot_HSapiens-BSA_lib.tsv.speclib

Command-line: C:\Users\bio\AppData\Local\Apps\2.0\85E7K1EH.CDH\TM9Z0EW0.O9E\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\BlibBuild -s -A -H -v warn -o -c 0.95 -i GT240313_c_Skyline -S "E:\THOG\GT240313_c\Skyline\GT240313_c-Skyline.redundant202404240847.stdin.txt" "E:\THOG\GT240313_c\Skyline\GT240313_c-Skyline.redundant.blib"
Working directory: E:\THOG\GT240313_c\Skyline
---------------------------
OK More Info
---------------------------
System.IO.IOException: ERROR: unable to handle mod in library entry: AAAHHYGAQC(Unimod:4)DK3
ERROR: reading file Swissprot_HSapiens-BSA_lib.tsv.speclib

Command-line: C:\Users\bio\AppData\Local\Apps\2.0\85E7K1EH.CDH\TM9Z0EW0.O9E\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\BlibBuild -s -A -H -v warn -o -c 0.95 -i GT240313_c_Skyline -S "E:\THOG\GT240313_c\Skyline\GT240313_c-Skyline.redundant202404240847.stdin.txt" "E:\THOG\GT240313_c\Skyline\GT240313_c-Skyline.redundant.blib"
Working directory: E:\THOG\GT240313_c\Skyline
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\skyline_23_1\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 181
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_23_1\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 433
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161
---------------------------

Sorry for not providing the full set. The needed files are attached.

Maybe I have to add that I also tried to define <static_modification> in the .sky file via text editor as suggested in this community request: https://skyline.ms/announcements/home/support/thread.view?rowId=6945

It seems that skyline accepts the modifications (no error msg) but the import still fails (modified .sky also in zip)

Gianin

Follow-up info:

I just tried to import the speclib featuring customized PTMs as well as UniMod:4 (this time spelled correctly). Now Skyline accepts the UniMod but gives the same error msg as above for the customized PTM.

Hi,

Currently Skyline/BiblioSpec doesn't support custom modifications (I guess you specified it with --var-mod or --mod on the command-line?). I don't see a straightforward way to add support for named custom mods either because as far as I can tell, the definitions of the custom mods used are not recorded in the speclib file or the report TSV. It wouldn't be too hard to add support for custom mods specified as masses though (i.e. the name would be the mass, like "--mod 123.4,123.4" instead of "--mod myModName,123.4" - I assume DIA-NN would accept that but I haven't tested). BiblioSpec could pass those through to Skyline as masses and let Skyline match them to a name. But for now, neither custom mod format is supported.