Do you have a .pdResultDetails file in addition to the .pdResult file?
In order for BiblioSpec to recognize that a file is PD 3.1, the .pdResultDetails file needs to be present in addition to the .pdResult file.
If the .pdResultDetails file is not present, then you get the error about "MassSpectrumItems" because BiblioSpec acts like it's the older format.

We should probably fix this so that BiblioSpec gives you an error message about not finding the .pdResultDetails file.

By the way, it sounds like you tried to attach a file, but no file got attached. This happens if the file you were trying to attach is over the 50MB limit.

In the future, if you need to send us files that are larger than that you can upload them here:
https://skyline.ms/files.url
-- Nick

Hi NIck,

Yes the details file is present as well. I have attached the error message again as I had a go at moving the PDResult file into the same folder as the raw files but didn't move the details file. Below is the error message generated despite the details file being present. Apologies if this is confusing.

Thanks for your help

Andrew

---------------------------
Skyline
---------------------------
ERROR: no such table: details.MassSpectrumItems

Command-line: C:\Users\andrew.williamson\AppData\Local\Apps\2.0\TK8TBECA.7R5\5E0Q6O8J.JE3\skyl..tion_9286511f3362df93_0019.0001_31a2f7d2aa6cc5be\BlibBuild -s -A -H -o -c 0.95 -i MCF7_Essen_AJKW -S "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant202508150236.stdin.txt" "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant.blib"
Working directory: C:\Temp raw file to analyse\Sellar_GPF_Data_350_1200mz\Sellar_GPF_Data_350_1200mz\Essen_GPF
Exit code: 1
---------------------------
OK More Info
---------------------------
Skyline (64-bit) 25.1.0.142 (7401c644b4)

System.IO.IOException: ERROR: no such table: details.MassSpectrumItems

Command-line: C:\Users\andrew.williamson\AppData\Local\Apps\2.0\TK8TBECA.7R5\5E0Q6O8J.JE3\skyl..tion_9286511f3362df93_0019.0001_31a2f7d2aa6cc5be\BlibBuild -s -A -H -o -c 0.95 -i MCF7_Essen_AJKW -S "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant202508150236.stdin.txt" "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant.blib"
Working directory: C:\Temp raw file to analyse\Sellar_GPF_Data_350_1200mz\Sellar_GPF_Data_350_1200mz\Essen_GPF
Exit code: 1 ---> System.IO.IOException: ERROR: no such table: details.MassSpectrumItems

Command-line: C:\Users\andrew.williamson\AppData\Local\Apps\2.0\TK8TBECA.7R5\5E0Q6O8J.JE3\skyl..tion_9286511f3362df93_0019.0001_31a2f7d2aa6cc5be\BlibBuild -s -A -H -o -c 0.95 -i MCF7_Essen_AJKW -S "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant202508150236.stdin.txt" "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant.blib"
Working directory: C:\Temp raw file to analyse\Sellar_GPF_Data_350_1200mz\Sellar_GPF_Data_350_1200mz\Essen_GPF
Exit code: 1

Output:
Reading results from 20250709_Stellar_colab_Test_Sample1_400ng-(3).pdResult.
ERROR: no such table: details.MassSpectrumItems
100%

 ---> System.IO.IOException: ERROR: no such table: details.MassSpectrumItems

Command-line: C:\Users\andrew.williamson\AppData\Local\Apps\2.0\TK8TBECA.7R5\5E0Q6O8J.JE3\skyl..tion_9286511f3362df93_0019.0001_31a2f7d2aa6cc5be\BlibBuild -s -A -H -o -c 0.95 -i MCF7_Essen_AJKW -S "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant202508150236.stdin.txt" "C:\Temp raw file to analyse\Essen\Skyline_MCF7_IonOpticks_MKU_DIANN_Run.sky\MCF7_Essen_AJKW.redundant.blib"
Working directory: C:\Temp raw file to analyse\Sellar_GPF_Data_350_1200mz\Sellar_GPF_Data_350_1200mz\Essen_GPF
Exit code: 1
   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\skyline_25_1\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 206
   --- End of inner exception stack trace ---
   --- End of inner exception stack trace ---
   at pwiz.Common.SystemUtil.ProcessRunner.ThrowExceptionWithOutput(Exception exception, String output) in C:\proj\skyline_25_1\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 266
   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\skyline_25_1\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 248
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_25_1\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 493
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 152
---------------------------

Hi, I was wondering if you had any other advice you could give me regarding this issue. Thanks Andrew

Can you send us the file "20250709_Stellar_colab_Test_Sample1_400ng-(3).pdResult" and "20250709_Stellar_colab_Test_Sample1_400ng-(3).pdResultDetails"?
The maximum size of a file that can be attached to one of these support requests is 50MB.
If those files are bigger than that you can upload them here:
https://skyline.ms/files.url
-- Nick

Thanks Nick, all uploaded using the link you sent.

Thank you for sending those files.
I am not sure, but I think the problem might be that these files are Proteome Discoverer version 3.2, and it might be that we only know how to read Proteome Discoverer version 3.1.
If that is the case, I imagine it might take us a few weeks to fix this.
-- Nick

Thanks for your help NIck.

Hi Nick,
I have realised I have been a bit silly. I had left the "Spectra to store" in the Spectrum Selector to none. I have changed this and the import works.
Sorry for wasting your time and thanks for your help
Andrew

Thanks for the update Andrew. I will add a check in the pdResult reader that if MassSpectrumItems is missing, then the user needs to export again with "Spectra to store" set properly. What's the correct value?

Thanks Matt.The correct value is "All".

Best wishes

Andrew