Overview
MSHub-GC separates overlapping GC-MS signals computationally. Its GNPS2 workflow produces deconvolved spectra, a quantification table and a cluster summary. These outputs support subsequent library searching and molecular networking in the GC-MS analysis ecosystem.
What can this tool do?
Common uses
- Recover component spectra from overlapping GC-MS chromatographic signals.
- Prepare quantitative and spectral outputs for downstream annotation.
Scientific fit
Primary function
Preprocessing and feature extraction
Other functions
Molecular networking and chemical similarity, Spectral processing and comparison
Analysis types
Untargeted metabolomics, Volatilomics
Data compatibility
Inputs
Raw instrument data, Mass spectra
Outputs
Feature or peak table, Mass spectra, Human-readable report
Input formats
netCDF or CDF, mzML, mzXML
Output formats
Deconvolved GC-MS spectra and downloadable tables
Scope and considerations
Designed for
- Untargeted GC-MS processing, including volatile-metabolite studies.
Not designed for
- LC-MS/MS feature processing or automatic confirmation of every compound identity.
Important requirements
- GC-MS files in CDF, mzML or mzXML format, with one format used throughout the input folder.
- The correct chromatographic time unit and a GNPS2 account.
Considerations
- Inspect deconvolution quality and chromatographic separation before interpreting component spectra.
- The linked paper describes the wider processing-and-networking system; the current launch page is the deconvolution workflow.
- Do not assume support for every vendor-native file type; confirm conversion and input compatibility in the current documentation.
Access and documentation
GNPS2 is openly available to the academic community. The current GNPS2 documentation asks industry users to contact the maintainers or UC Riverside Technology Transfer regarding organizational access. Workflow submission requires a GNPS2 account. The linked workflow repository is public; this hosted-service entry does not assert a license for every bundled processing dependency.
Evidence and review
Editorial review of official documentation, repository and the direct tool publication on 2026-09-10. No analysis job, independent benchmark or developer verification was performed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Aksenov AA, et al. Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data. Nature Biotechnology 39, 169–173 (2021). doi:10.1038/s41587-020-0700-3
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-10 · First committed entry
Add three GNPS2 Tools and expose complete related-tool lists
View change · Entry at this revision