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guest
2023-01-29
Error in Importing Files
   Cannot build library from Peptide Shaker mzid?

Error in Importing Files


Hi,

 

I am getting following error in all the Skylines software that I use. I am requesting suggestion for that.

Here is the error message.

At 3:31 PM:
To extract chromatograms from C:\Users\Protein.Shared\Desktop\HPV\171020_Caski_Heavy_only.raw full-scan settings must be enabled.


Inner exceptions:
Exception type: pwiz.Skyline.Model.Results.NoFullScanFilteringException
Error message: To extract chromatograms from C:\Users\Protein.Shared\Desktop\HPV\171020_Caski_Heavy_only.raw full-scan settings must be enabled.
To extract chromatograms from C:\Users\Protein.Shared\Desktop\HPV\171020_Caski_Heavy_only.raw full-scan settings must be enabled.
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider..ctor(MsDataFileImpl dataFile, ChromFileInfo fileInfo, SrmDocument document, IRetentionTimePredictor retentionTimePredictor, String cachePath, IProgressStatus status, Int32 startPercent, Int32 endPercent, IProgressMonitor loader) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 92
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateSpectraChromProvider(MsDataFileImpl dataFile, ChromFileInfo fileInfo) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1263
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 249




Cannot build library from Peptide Shaker mzid?


Hi Skyline team,

I am trying to build a spectral library from Peptide Shaker output. I have test PeptideShaker 2.0.14, 2.0.16 and 2.0.18 with the same error. I tried both my search result or the example packaged with PeptideShaker. The Skyline version I am using is Skyline (64-bit) 20.2.0.343 (a7a9e8c4f). 

The error message is,

System.IO.IOException: ERROR: No spectra were found for the new library.

Command-line: C:\Users\ht\AppData\Local\Apps\2.0\8MPRNX2K.0X7\9EA9LC5J.M7P\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0.99 -i testShakerOut -K -S "C:\Users\ht\AppData\Local\Temp\tmp5FE4.tmp" "C:\Users\ht\Desktop\MS_tools\PeptideShaker-2.0.16\resources\example_dataset\data\testShakerOut.redundant.blib"
Working directory: C:\Users\ht\Desktop\MS_tools\PeptideShaker-2.0.16\resources\example_dataset\data
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 62
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 156

 

To reproduce the error, the mzid was generated using PeptideShaker 2.0.16 -> Open Example -> Export -> Follow Up Analysis -> Skyline Export - Export as mzid -> save to "PeptideShaker-2.0.16\resources\example_dataset\data\", files of type set to mzIdentML v1.1

 

What can I do to solve this problem?

Thank you.