Add support for DIA-NN

Add support for DIA-NN Yishai  2022-03-14

Hi, is it possible for Skyline to support importing search results from DIA-NN? Particularly for DIA-PASEF.


Yishai responded:  2022-03-14

When trying to create a library using the DIA-NN speclib file I get the error below, even though the pro.tsv file is in the same directory:

System.IO.IOException: ERROR: unable to determine DIA-NN report filename for 'pro.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)

Command-line: C:\Users\bsyishai\AppData\Local\Apps\2.0\97PPYED4.EZC\8W6H8HGX.8MW\skyl..tion_e4141a2a22107248_0015.0002_38ac599f018d3163\BlibBuild -s -A -H -o -c 0.95 -i 15384 -S "C:\Users\bsyishai\AppData\Local\Temp\tmp4F6F.tmp" "H:\Proteomics\Projects\RnD\Alternative_enzymes\INCPM_15384\DIA\DIA-NN\15384.redundant.blib"
Working directory: H:\Proteomics\Projects\RnD\Alternative_enzymes\INCPM_15384\DIA\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

Nick Shulman responded:  2022-03-14
When you are building a spectral library from DIA-NN search results, BiblioSpec needs to be able to find another file whose name ends with ".tsv".
BiblioSpec is never sure what the exact name of that ".tsv" file is going to be, but BiblioSpec tries to find the file whose name has the most letters in common with the original .speclib file.

Which other files do you have in the same folder as your .speclib file?
-- Nick