What does this strategy enable?
Reverse metabolomics reverses the usual untargeted workflow. Instead of starting with an unknown feature and attempting to infer its structure, the researcher begins with a candidate structure and an experimental MS/MS spectrum, searches public metabolomics data for matching spectra, and then uses repository metadata to ask where the molecule occurs. The resulting organism, biospecimen, phenotype or disease associations can guide biological validation.
Transferable workflow
Workflow
- 1
Generate or obtain a reference MS/MS spectrum
Acquire tandem mass spectra for a candidate chemical structure, for example from a synthesized standard, authenticated standard, or suitable reference source.
- 2
Select a representative reference spectrum
When standards are analyzed in mixtures, automatically select the MS/MS scan associated with the expected precursor and review the spectrum before repository searching.
- 3
- 4
Contextualize matches with sample metadata
Summarize organism, biospecimen, phenotype, disease state and other standardized metadata associated with matching public files.
- 5
Prioritize biological associations
Use the distribution of matched spectra across public datasets to generate hypotheses about where the molecule occurs and which phenotypes or sample types it may be associated with.
- 6
Validate prioritized associations
Test the proposed association in independent cohorts, targeted measurements, culture systems, or functional experiments appropriate to the biological question.
Connected resources
Tools used in this strategy
Strategy profile
Related objectives
Phenotype association, Molecular discovery, Metabolite annotation
Components
Data acquisition, Spectral search, Repository-scale mining, Metadata analysis, Biological validation, Data and workflow sharing
Sample types
Feces or stool, Tissue or biopsy, Microbial culture or biomass, Synthetic or analytical standards, Other or broadly applicable
Biological context
Human, Animal, Microbial, Host–microbe interaction, Synthetic or reference material, Broadly applicable
Organisms
Homo sapiens
Ion mobility
Ion mobility not required
Scope and considerations
Designed for
- Asking where a known or newly synthesized chemical structure occurs across existing untargeted MS/MS datasets.
- Using repository-scale metadata to generate hypotheses linking a molecule to organisms, sample types, disease states or other phenotypes.
Important requirements
- A suitable reference MS/MS spectrum for the candidate molecule.
- Public datasets with matching MS/MS signals and sufficient metadata to interpret biological context.
Considerations
- A repository spectral match is evidence of spectral similarity and occurrence, not by itself a complete structural confirmation.
- Repository composition and metadata coverage can bias which biological contexts are visible.
Reusable resources
Publication
Gentry EC, Collins SL, Panitchpakdi M, et al. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626, 419–426 (2024).