MetaboLights

What MetaboLights is

MetaboLights is a repository and reference knowledge base for metabolomics studies across multiple species and analytical platforms. Founded in 2012 and maintained by the European Bioinformatics Institute (EMBL-EBI) with funding from the Biotechnology and Biological Sciences Research Council (BBSRC), the resource provides a public home for sharing primary experimental data, protocols, and metadata.

The platform addresses the challenge of making metabolomics findings systematically searchable and reusable. It combines raw analytical datasets—specifically from nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry—with a reference knowledge layer detailing individual metabolite compounds, their biological roles, anatomical locations, and physiological concentrations.

How it is organised

The database is structured into two interconnected tiers: a repository for complete experimental datasets and a reference layer for curated compound properties. Authors submit studies using a guided workflow structured around the ISA-TAB format, ensuring submissions adhere to Metabolomics Standards Initiative (MSI) recommendations. Each accepted submission receives a permanent accession identifier, such as MTBLS1.

Data curation incorporates controlled vocabularies and ontologies, including the BRENDA tissue ontology for anatomical contexts and the NCBI taxonomy for species classification. Metabolite chemical structures are interconnected with external chemistry repositories including ChEBI, PubChem, and ChemSpider. Datasets, including raw analytical files, are distributed via an FTP server.

Key facts

What you can use it for

Study data deposition

Depositing metabolomics raw files, protocols, and study designs to acquire a stable accession number required by scientific journals.

Metabolite reference lookup

Consulting reference spectra, chemical structures, biological roles, locations, and concentrations for specific chemical compounds.

Secondary analysis of metabolomics data

Downloading primary mass spectrometry and NMR spectroscopy datasets via FTP to reanalyse published cross-species studies.

Query it here

The research agent queries MetaboLights directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.

Strengths and limits

Questions