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No Spectra jessica chapman  2023-05-11
 
Hello,

I am trying to build a spectral library from a Peaks search result. I exported the pepxml file and even set the score cutoff to 1 to test if that was the issue, but I keep getting the same error. The raw data is just PRTC that we use for QC, but run on a timsTOF HT. The search is against just a PRTC peptide containing library.

Our other instrumentation is thermo so I have used proteome discoverer outputs to build spectral library. In the past I have build spectral libraries from other search outputs and this is my first time using Peaks so I am likely making a silly mistake. I have attached the pepxml file.

Thank you for your help!



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Skyline
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ERROR: No spectra were found for the new library.

Command-line: C:\Users\chapmanj\AppData\Local\Apps\2.0\1B2GTZ0C.LN3\5LA21DVE.A9O\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\BlibBuild -s -A -H -o -i PRTC_timsTOF -S "C:\Users\chapmanj\AppData\Local\Temp\tmpD567.tmp" "Z:\Proteomics\Skyline Files\Spectral Libraries\PRTC_timsTOF.redundant.blib"
Working directory: X:\Clinical Protemics Lab Quality Control\QC_Development\timTOF PRTC\PRTC_timsTOF_DDA\Analysis 1
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OK More Info
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System.IO.IOException: ERROR: No spectra were found for the new library.

Command-line: C:\Users\chapmanj\AppData\Local\Apps\2.0\1B2GTZ0C.LN3\5LA21DVE.A9O\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\BlibBuild -s -A -H -o -i PRTC_timsTOF -S "C:\Users\chapmanj\AppData\Local\Temp\tmpD567.tmp" "Z:\Proteomics\Skyline Files\Spectral Libraries\PRTC_timsTOF.redundant.blib"
Working directory: X:\Clinical Protemics Lab Quality Control\QC_Development\timTOF PRTC\PRTC_timsTOF_DDA\Analysis 1
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_22_2\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 161
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_22_2\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 412
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161
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Nick Shulman responded:  2023-05-11
BiblioSpec does not know what to do with a file whose name ends in ".mzidentml.xml".
If you changed the name for "db.mzid", it might work.

When BiblioSpec creates a spectral library from either db.pep.xml or your renamed "db.mzid", BiblioSpec is going to be looking for a file whose name starts with "PRTC_30min_1column_Slot1-4_1_186" in order to find the spectra to put in the spectral library.

I believe that the "ERROR: No spectra were found for the new library." often means that the spectrum IDs in the pep.xml file are not in the correct format given the raw file that BiblioSpec is trying to read the spectra from.

If you send us your file "PRTC_30min_1column_Slot1-4_1_186.d" or "PRTC_30min_1column_Slot1-4_1_186.mzML", we could try to reproduce this problem and might be able to give you more information about what is going wrong.

Files which are less than 50MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick
 
jessica chapman responded:  2023-05-11

Hi Nick

Thank you for your quick response.

I researched the data separately as I had previously group 4 raw files. I tried to create a spectral library again using the newly exported pepxml. The same error occurs. I wanted to try this before bugging you again. I am going to upload the file: PRTC_30min_1column_Slot1-4_1_191.d and the new pepxml file I exported is attached here.
 
jessica chapman responded:  2023-05-12

Hi Nick

I reached out to the Peaks Studio support and found out the current export options in Peaks Studio 11 does not export the mzXML so it won't work for library generation. They are correcting this in a version that will be released at ASMS. I went ahead and ran the same data through a different search engine and built a library that way.

Thank you for your help!

Take Care
Jessica