I exported the DDA searched result form PEAKS as .pep.xml file. I tried to build library with this file. Skyline gave this errors.
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Skyline
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ERROR: While searching for spectrum file for the search results file 'db.pep.xml', could not find matches for the following basename with any of the supported file extensions (.mz5, .mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
ERROR: 20230627_Hela_100pg_30min_DDA_S6-A2_1_1998.d
ERROR:
ERROR: In any of the following directories:
ERROR: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export\Hela_DDA_iRT\Analysis 1
ERROR: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export\Hela_DDA_iRT
ERROR: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export
Command-line: C:\Users\guox1\AppData\Local\Apps\2.0\WM57MYLB.LYN\PJPQK28Q.Y0J\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\BlibBuild -s -A -H -o -i Peaks -S "C:\Users\guox1\AppData\Local\Temp\tmpE499.tmp" "C:\Users\guox1\Documents\Projects\Single_Cell\Skyline\Library\Peaks.redundant.blib"
Working directory: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export\Hela_DDA_iRT\Analysis 1
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OK More Info
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System.IO.IOException: ERROR: While searching for spectrum file for the search results file 'db.pep.xml', could not find matches for the following basename with any of the supported file extensions (.mz5, .mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
ERROR: 20230627_Hela_100pg_30min_DDA_S6-A2_1_1998.d
ERROR:
ERROR: In any of the following directories:
ERROR: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export\Hela_DDA_iRT\Analysis 1
ERROR: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export\Hela_DDA_iRT
ERROR: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export
Command-line: C:\Users\guox1\AppData\Local\Apps\2.0\WM57MYLB.LYN\PJPQK28Q.Y0J\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\BlibBuild -s -A -H -o -i Peaks -S "C:\Users\guox1\AppData\Local\Temp\tmpE499.tmp" "C:\Users\guox1\Documents\Projects\Single_Cell\Skyline\Library\Peaks.redundant.blib"
Working directory: Y:\FPL_users\GuoXue\Single_Cell\Hela_Gradient_Test\Peaks_export\Hela_DDA_iRT\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: |
2023-06-30 07:14 |
If you have a folder on your computer called "20230627_Hela_100pg_30min_DDA_S6-A2_1_1998.d", you should copy that folder into the same folder as your pep.xml file "'db.pep.xml".
When you import peptide search results into Skyline, Skyline creates a BiblioSpec spectral library from the peptide search results. The pep.xml file says which peptides were found in which spectra. BiblioSpec also needs to know what the spectrum looks like, which is information that is not contained in the pep.xml file.
BiblioSpec is trying to find the mass spec data file that goes with the pep.xml file.
BiblioSpec knows that the mass spec data file's name starts with "20230627_Hela_100pg_30min_DDA_S6-A2_1_1998.d". The file's name might end with any of a list of possible extensions including ".mzML" or ".d".
-- Nick |
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| guo xue responded: |
2023-07-02 20:52 |
Hi Nick, Thank you for your respond. I followed your suggestion and this time it doesnt have error. However one it starts to build library, it will take forever to read spectra and I can't use the library at all. I put the all the files at local drive already but it didnt improve. Do you know what is the reason? should I just wait?
Thank you. |
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| guo xue responded: |
2023-07-02 22:06 |
hello, the building was finished. but it shows this error.
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Skyline
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ERROR: No spectra were found for the new library.
Command-line: C:\Users\guox1\AppData\Local\Apps\2.0\WM57MYLB.LYN\PJPQK28Q.Y0J\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\BlibBuild -s -A -H -o -i Hela_5ng_test -S "C:\Users\guox1\AppData\Local\Temp\tmp6B66.tmp" "C:\Users\guox1\Documents\Projects\Single_Cell\Skyline\Library\Hela_5ng_test.redundant.blib"
Working directory: C:\Users\guox1\Documents\Projects\Single_Cell\Skyline\Peaks_Export
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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\guox1\AppData\Local\Apps\2.0\WM57MYLB.LYN\PJPQK28Q.Y0J\skyl..tion_e4141a2a22107248_0016.0002_6388bc76fc4672e2\BlibBuild -s -A -H -o -i Hela_5ng_test -S "C:\Users\guox1\AppData\Local\Temp\tmp6B66.tmp" "C:\Users\guox1\Documents\Projects\Single_Cell\Skyline\Library\Hela_5ng_test.redundant.blib"
Working directory: C:\Users\guox1\Documents\Projects\Single_Cell\Skyline\Peaks_Export
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: |
2023-07-03 06:01 |
When it takes a really long time and you eventually get the "No spectra were found for the new library", the problem is that BiblioSpec does not understand the spectrum identifiers in the peptide search results.
There was another support request where someone else using PEAKS ran into the exact same behavior:
https://skyline.ms/announcements/home/support/thread.view?rowId=24811
We have not yet come up with a solution to this problem.
I will ask my coworkers and try to find someone who will be able to tell you what you can do about this.
-- Nick |
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