Errors happened when Skyline (21.1.9.348) builds the spectral library using the speclib generated by DIA-NN.

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Errors happened when Skyline (21.1.9.348) builds the spectral library using the speclib generated by DIA-NN. andyzcq  2021-12-14
 
I used the latest version of skyline to build the spectral library based on the speclib file generated by DIA-NN, as the version3 speclib has been supported by Skyline (21.1.9.348) according to the update log.

Errors happened, and the errors are shown below.

"---------------------------
Skyline-daily
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ERROR: could not find precursorId '(UniMod:1)SDS(UniMod:21)GEQNYGERES(UniMod:21)R2' in speclib; is 'DDA_library_DeepLearning-first-pass.tsv' the correct report TSV file?
ERROR:
ERROR: reading file DDA_library_DeepLearning-lib.tsv.speclib

Command-line: C:\Users\zcq\AppData\Local\Apps\2.0\15HT56TR.XZ7\XGZRPD5Q.HLT\skyl..tion_e4141a2a22107248_0015.0001_4fbcbec802624e1e\BlibBuild -s -A -H -o -c 0 -i 1 -S "C:\Users\zcq\AppData\Local\Temp\tmpDE3A.tmp" "D:\project\SCASP_PTM\20210923_HeLa_polyIC_CaTiO3\skyline\1.redundant.blib"
Working directory: D:\project\SCASP_PTM\20210923_HeLa_polyIC_CaTiO3\DIA-NN
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OK More Info
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System.IO.IOException: ERROR: could not find precursorId '(UniMod:1)SDS(UniMod:21)GEQNYGERES(UniMod:21)R2' in speclib; is 'DDA_library_DeepLearning-first-pass.tsv' the correct report TSV file?
ERROR:
ERROR: reading file DDA_library_DeepLearning-lib.tsv.speclib

Command-line: C:\Users\zcq\AppData\Local\Apps\2.0\15HT56TR.XZ7\XGZRPD5Q.HLT\skyl..tion_e4141a2a22107248_0015.0001_4fbcbec802624e1e\BlibBuild -s -A -H -o -c 0 -i 1 -S "C:\Users\zcq\AppData\Local\Temp\tmpDE3A.tmp" "D:\project\SCASP_PTM\20210923_HeLa_polyIC_CaTiO3\skyline\1.redundant.blib"
Working directory: D:\project\SCASP_PTM\20210923_HeLa_polyIC_CaTiO3\DIA-NN
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 149
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157
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Nick Shulman responded:  2021-12-14
I do not know what is going wrong, but if you send us your files we can figure it out.
It sounds like we would need to see the files "DDA_library_DeepLearning-first-pass.tsv" and "DDA_library_DeepLearning-lib.tsv.speclib".
If those files are less than 50MB you can attach them to this support request.
You can upload larger files here:
https://skyline.ms/files.url

By the way, is "DDA_library_DeepLearning-first-pass.tsv" the TSV file which is supposed to go with "DDA_library_DeepLearning-lib.tsv.speclib"? BiblioSpec seems to have a complicate way of figuring out which TSV file is the report TSV for a particular speclib. BiblioSpec tries to find the TSV file whose name has the most common letters at the start in common with the speclib filename, and which also has a column named "Precursor.Id".
-- Nick
 
andyzcq responded:  2021-12-14
I have uploaded two files to the server.

"DDA_library_DeepLearning-first-pass.tsv" go with the spclib file. But in the same folder, there are many files whose filenems are common with the start of the speclib filename.
 
Nick Shulman responded:  2021-12-15
Can you zip up and send us all of the .tsv files from that folder?
My guess is that one of those other .tsv files is the actual one that BiblioSpec is supposed to use.

If the problem is that BiblioSpec is using the wrong .tsv file, then you can work around this problem by deleting all of the .tsv files from that folder except for the one that is supposed to be used as the report file for the speclib file.

I am not the expert on this area of code, so I do not actually know what is going on, or what the report file is supposed to look like.
Someone else might be able to give you a better answer in a few hours.
-- Nick
 
andyzcq responded:  2021-12-15
I have zipped all tsv files whose name is DIA-NN and uploaded it to the server.
 
Nick Shulman responded:  2021-12-15
Thanks for sending those files.

If the only two files that were in the directory were "DDA_library_DeepLearning.tsv" and "DDA_library_DeepLearning-lib.tsv.speclib" then BiblioSpec would be able to build the library for you.

The other tsv files in that folder, specifically "DDA_library_DeepLearning-first-pass.pr_matrix.tsv", "DDA_library_DeepLearning-first-pass.tsv" and
"DDA_library_DeepLearning.pr_matrix.tsv" are causing BiblioSpec to choose incorrectly.

Hope this helps,
I am not sure whether BiblioSpec can be improved so that this workaround would not be necessary when there are tsv files from two different .speclib's in the same folder.
-- Nick
 
andyzcq responded:  2021-12-15
Great!

I have successfully built the spectral library following your suggestion.

Thanks, Nick.
 
matt.chambers42 responded:  2021-12-16
BiblioSpec will ignore the "-first-pass" files in the next release and next Skyline-daily. I hadn't tried a two-pass search before so I didn't know about those files. Thanks for the report!