Questions about the spectral library build by DIA-NN speclib file.

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Questions about the spectral library build by DIA-NN speclib file. andyzcq  2022-03-20
 

I have successfully built the spectral library based on DIA-NN speclib file, and found the peptides with N-terminal acetylation can not be recognized by Skyline.

See attachment.

 
 
Nick Shulman responded:  2022-03-20
I am not the expert on BiblioSpec, but I don't think modifications are supposed to look like that, with the square brackets appearing before the first amino acid in the sequence. With N-terminal modifications, my understanding was that they were supposed to look to Skyline as if they were attached to the first amino acid, so the square brackets are supposed to go after the first amino acid.

There might be a bug in terms of what BlibBuild.exe is putting into the .blib file when you are building the spectral library from your DIA-NN results.

Can you send us your .speclib file? If that file is less than 50MB you can attach it to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick
 
andyzcq responded:  2022-03-21
I have attached the spclib file.
 
Nick Shulman responded:  2022-03-21
Oops. I also need the report .tsv file that goes with that. If you're not sure which .tsv file is the one that BiblioSpec ends up using, I guess you can zip up all of the files which are in the same folder as the .speclib file.
While you are at it, it would probably also be helpful to see your Skyline document and the library that you built.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries.
-- Nick
 
andyzcq responded:  2022-03-21
I attached the tsv file and uploaded the Skyline ducument to the server.
 
Nick Shulman responded:  2022-03-22
I do not see the .tsv file attached. I only see "Library-free-lib.tsv.speclib".
When I tell BiblioSpec to build a library from "Library-free-lib.tsv.speclib", I am getting the usual error:

ERROR: unable to determine DIA-NN report filename for 'Library-free-lib.tsv.speclib': the TSV report is required to read speclib files and must be in the same directory as the speclib and share some leading characters (e.g. somedata-tsv.speclib and somedata-report.tsv)

(If you tried to attach the .tsv file to this support request, and it did not work, that usually means that the file was larger than 50MB and could not be attached. You can upload larger files here: https://skyline.ms/files.url )
-- Nick
 
andyzcq responded:  2022-03-22
Hi, Nick,
I have uploaded the tsv file to the server.