Hi, I am running MS-DIAL Console App v5.5 (MSDIAL.console.v5.5.260323-linux-net8) on Ubuntu 22.04 (WSL2) and encountering an issue where the MSP spectral library is not being loaded during GC-MS annotation, resulting in all peaks being reported as "Unknown".
Environment:
OS: Ubuntu 22.04 (WSL2 on Windows)
MS-DIAL version: v5.5.260323 (linux-net8 build)
Data format: ABF
Ion mode: Positive, Centroid, GC-MS
Parameter file (relevant section):
MSP file: /home/melody/msdial/libraries/NIST20_combined.msp
Retention type: RT
EI similarity tolerance for identification: 80
Identification score cut off: 70
What happens:
The pipeline runs successfully through peak picking, deconvolution, and alignment for all 4 samples. However, all features in the output .mdalign file have Metabolite name: Unknown and Total score: null. When grepping the log output for any MSP/library/database-related messages, only Annotation started is printed — there is no indication that the MSP file is ever read or loaded.
I also tested with a minimal 2-compound MSP file to rule out library format issues, but the result was the same — no compounds were matched.
The run always ends with the following error during mzTab export:
System.NullReferenceException: Object reference not set to an instance of an object.
at CompMs.MsdialCore.Export.MztabFormatExporter.SetOntology(AlignmentSpotProperty spot)
This suggests the annotation result object is null, consistent with the MSP library not being loaded at all.
Question:
Is GC-MS MSP library annotation supported in the Linux build of the Console App v5.5? If so, is there a known issue with the MSP file path parsing on Linux, or a workaround to get annotation working?
Thank you.
Msdial-GCMS-Param.txt
Hi, I am running MS-DIAL Console App v5.5 (MSDIAL.console.v5.5.260323-linux-net8) on Ubuntu 22.04 (WSL2) and encountering an issue where the MSP spectral library is not being loaded during GC-MS annotation, resulting in all peaks being reported as "Unknown".
Environment:
OS: Ubuntu 22.04 (WSL2 on Windows)
MS-DIAL version: v5.5.260323 (linux-net8 build)
Data format: ABF
Ion mode: Positive, Centroid, GC-MS
Parameter file (relevant section):
MSP file: /home/melody/msdial/libraries/NIST20_combined.msp
Retention type: RT
EI similarity tolerance for identification: 80
Identification score cut off: 70
What happens:
The pipeline runs successfully through peak picking, deconvolution, and alignment for all 4 samples. However, all features in the output .mdalign file have Metabolite name: Unknown and Total score: null. When grepping the log output for any MSP/library/database-related messages, only Annotation started is printed — there is no indication that the MSP file is ever read or loaded.
I also tested with a minimal 2-compound MSP file to rule out library format issues, but the result was the same — no compounds were matched.
The run always ends with the following error during mzTab export:
System.NullReferenceException: Object reference not set to an instance of an object.
at CompMs.MsdialCore.Export.MztabFormatExporter.SetOntology(AlignmentSpotProperty spot)
This suggests the annotation result object is null, consistent with the MSP library not being loaded at all.
Question:
Is GC-MS MSP library annotation supported in the Linux build of the Console App v5.5? If so, is there a known issue with the MSP file path parsing on Linux, or a workaround to get annotation working?
Thank you.
Msdial-GCMS-Param.txt