MetaboLights: a database for metabolomics experiments and derived information

MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals.

We offer user-submission tools and have strong reporting capabilities. We use and further develop de-facto standard formats where various components are encapsulated, such as the encoded spectral and chromatographic data, and associated information about the chemical structure, as well as metadata describing assays and the study as a whole.

MetaboLights semantic quality is based on various controlled vocabularies and ontologies linking data to existing resources such as BRENDA.
We collaborate closely with major parties in world-wide metabolomics communities, such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

We are always looking at ways to improve MetaboLights. Please send your feedback in the form here or email us directly at


Scientific Advisory Board

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Citing MetaboLights
Kenneth Haug, Keeva Cochrane, Venkata Chandrasekhar Nainala, Mark Williams, Jiakang Chang, Kalai Vanii Jayaseelan, Claire O’Donovan.
MetaboLights: a resource evolving in response to the needs of its scientific community.

Nucleic Acids Research, gkz1019, doi:10.1093/nar/gkz1019, PMID:31691833.
All data is governed by the EMBL-EBI's Terms of use and all code is licensed under Apache 2.0.

PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications.


MetaboLights submissions are powered by the ISA software suite. so experimental data gets submitted in ISA-Tab format. The Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies.

MetaboLights is the recommended Metabolomics repository for a number of leading journals.

Nature Scientific Data
BioMed Central
PLOS Biology
EMBO press
F1000 Research
Springer Link - Metabolomics
Wellcome Trust Open Research

Through the BioSharing initiative we continue to ensure that a growing number of journals that have data policies endorse MetaboLights as the recommended Metabolomics repository.

The Metabolomics team's activities are supported by the European Molecular Biology Laboratory (EMBL), Medical Research Council grant MR/L01632X/1, BBSRC grant BB/M027635/1, Wellcome Trust grant 202952/Z/16/Z, National Institutes of Health grant 1U54GM114833-01 and EC H2020 grants 634402 and 654241.

Past funding includes BBSRC grants BB/L024152/1, BB/I000933/1 and BB/N02342/1 and EC H2020 grant 654021.