You might find some useful information in the following support request:
https://skyline.ms/announcements/home/support/thread.view?rowId=59776

BiblioSpec is looking for a .tsv file where the first line of the file contains the names "Precursor.Id", "Q.Value" and "RT".
The file "Human_VR_SCPC9_MOLT4_MCF7_Plasma_HpH_48Fr.tsv" in your .rar file does not have any of those names, so BiblioSpec knows that that is not the file that it is looking for.

You probably have another .tsv file somewhere that does have those column names on its first line. If you rename that other file to "Human_VR_SCPC9_MOLT4_MCF7_Plasma_HpH_48Fr.tsv" you will probably be able to successfully import your DIA-NN results.
-- Nick

Thanks Nick I will look into this and report back..

Hi Nick,

I couldn't find another file with those headers so I've instead tried building the library from scratch in Skyline using the DDA search results from MSFragger ( in Fragpipe v20). I have both .pepxml as well as the corresponding calibrated/uncalibrated .mzmL files in the same folder but I'm getting a similar error when trying to import the results from the DDA-PASEF runs. I've uploaded the .pepxml and .mzmL file from one fraction for reference : https://drive.google.com/file/d/1jC1ewyHdL3AjXH3nUNAjf0aKZrlPoH_n/view?usp=sharing .

Thanks again for your help with this,
Vincent





Skyline-daily (64-bit) 23.1.1.268 (c58f1f56e)

System.IO.IOException: ERROR: While searching for spectrum file for the search results file 'EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560.pepXML', could not find matches for the following basename with any of the supported file extensions (_uncalibrated.mgf, _calibrated.mgf, .mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
ERROR: EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560
ERROR:
ERROR: In any of the following directories:
ERROR: C:\Users\Admin\Desktop\Test
ERROR: C:\Users\Admin\Desktop
ERROR: C:\Users\Admin

Command-line: C:\Users\Admin\AppData\Local\Apps\2.0\PE8R0MVM.K8V\BACJ7O8E.9JZ\skyl..tion_2e441fc3bf6adc7f_0017.0001_e4c70d6dfe97aa96\BlibBuild -s -A -H -v warn -o -c 0.95 -i test -S "C:\Users\Admin\Desktop\Test\test.redundant202310060417.stdin.txt" "C:\Users\Admin\Desktop\Test\test.redundant.blib"
Working directory: C:\Users\Admin\Desktop\Test
   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\pwiz\pwiz_tools\Shared\CommonUtil\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\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 433
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 161

I was able to get this to work by editing your .pepXML file and finding all of the places where it said:
base_name="D:\Data\EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560"
and changing them to:
base_name="D:\Data\EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560_uncalibrated"

The error message that you were getting was telling you that it was looking for a file whose name starts with "EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560" and is followed by any of a number of possible things including "_uncalibrated.mgf", "mzML", etc.

It would have been most happy if it could have found a file called "EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560_uncalibrated.mgf".
You wouldn't happen to have a file with that name somewhere that you could copy into the same folder as your pepXML file?

I see that you have a file called "EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560_uncalibrated.mzML". Unfortunately, BiblioSpec was not actually looking for a file with that name.
I tried copying "EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560_uncalibrated.mzML" to "EV001065_VR_MutaQuant_DDA-PASEF_60SPD_celllines_HpH_MCF7_F48_S5-H12_1_1560.mzML", but then I got the error message "To import an MSFragger search of timsTOF data (with ion_mobility attribute), the corresponding *_uncalibrated or *_calibrated MGF or mzML file is required."

I think there might be a bug in BiblioSpec that it should have been looking for a file whose name ended in "_uncalibrated.mzML" instead of just looking for "_uncalibrated.mgf").
I will ask around and see whether this is something we can fix.
-- Nick