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ERROR: No spectra were found for the new library

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ERROR: No spectra were found for the new library jianji chen  2023-10-02 13:11
 
Dear Skyline Support Team,
I was trying to search and build library from DDA files. However, I started receiving an error: "No spectra were found for the new library". I attached the error message below. Could you please advise how I should proceed? Thank you in advance!
BTW, I installed the most recent update today and got this error.
JC

Command-line: C:\Users\JianjiC\AppData\Local\Apps\2.0\K6LP5M3R.JC7\ONHT3JXM.TBV\skyl..tion_2e441fc3bf6adc7f_0017.0001_f0a1d88b2514a5aa\BlibBuild -s -A -H -v warn -o -c 0.95 -i HCP_Method_5_10 -S "C:\Users\XXX\HCP_Method_5_10.redundant202310020100.stdin.txt" "C:\Users\XXX\HCP_Method_5_10.redundant.blib"
Working directory: C:\Users\XXX\Raw\DOE
   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
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Nick Shulman responded:  2023-10-02 13:19
If you are performing a DDA search in Skyline, the usual reason to get that message would be that the peptide search engine really did not find any peptides in your raw files.
This might have something to do with the FASTA file that you provided, or it might be that the MS2 spectra in your raw file were of such low quality that no peptides could be detected.

If you would like, you could send us your raw files and your FASTA file, and we could try doing the same steps that you did and see whether it looks like Skyline is doing anything incorrect.

You could package your raw files and your FASTA file in a .zip file and upload it here:
https://skyline.ms/files.url

It would also be helpful if you could send us screenshots of the pages of the Import Peptide Search wizard so that we can see what your settings were so that we can reproduce your problem.

-- Nick
 
jianji chen responded:  2023-10-03 16:24
Thank you so much Nick for your prompt response. I got it working by resetting the peptide settings.
JC