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Error building spectral library from MSFragger Search with timstof data

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Error building spectral library from MSFragger Search with timstof data claire tonry  2021-09-07 03:47
 
Hi, I get the following error when I try to import the pep.xml file generated from an MSFragger search of timstof DDA data into Skyline

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Skyline
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ERROR: Could not find spectrum file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881[.mz5|.mzML|.mzXML|.ms2|.cms2|.bms2|.pms2|_uncalibrated.mgf|_calibrated.mgf]' for search results file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881.pepXML' in current directory, ../,../../.
ERROR:

Command-line: C:\Users\3053492\AppData\Local\Apps\2.0\5VYXQT5K.TNB\893P3P9W.TXB\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\BlibBuild -s -A -H -o -c 0.95 -i Skyline_Lib_Test_07092021 -S "C:\Users\3053492\AppData\Local\Temp\tmpEA60.tmp" "C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild\Skyline_Lib_Test_07092021.redundant.blib"
Working directory: C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild
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OK More Info
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System.IO.IOException: ERROR: Could not find spectrum file

'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881[.mz5|.mzML|.mzXML|.ms2|.cms2|.bms2|.pms2|_uncalibrated.mgf|_calibrated.mgf]' for search results file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881.pepXML' in current directory, ../,../../.
ERROR:

Command-line: C:\Users\3053492\AppData\Local\Apps\2.0\5VYXQT5K.TNB\893P3P9W.TXB\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\BlibBuild -s -A -H -o -c 0.95 -i Skyline_Lib_Test_07092021 -S "C:\Users\3053492\AppData\Local\Temp\tmpEA60.tmp" "C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild\Skyline_Lib_Test_07092021.redundant.blib"
Working directory: C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 65
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157
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Nick Shulman responded:  2021-09-07 05:57
That error message is telling you that it was not able to find the mass spec data file that goes with the .pep.xml.

The way that the error message is phrased is unfortunate. The "|" in the error message is supposed to be interpreted as the word "or".
So, what the error message is trying to tell you is that BiblioSpec was looking for a file whose name started with "A210120_ct_heart_FFPE_fracs_AF_F1_dda_881", and which might have ended with a filename extension like ".mzML", ".mzXML", or any of the other extensions listed there.

The error is also saying that it tried looking in the same folder that contained the pwpXML file, as well as the parent of that folder (".."), or the folder two levels up ("../..")

If you have a file called "A210120_ct_heart_FFPE_fracs_AF_F1_dda_881.mzML" you should copy it into the same folder as your pepXML file, and then it should work.

Here is the web page that tells you which files you need to have in which places depending on the type of peptide search results that you have:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

That page says that for MSFragger results, you should also be able to use the .raw file instead of .mzML, etc.
-- Nick