MetaboLights is EMBL-EBI’s public repository for metabolomics studies, hosting both the raw experimental data and the structured metadata that describe how it was produced. For a researcher choosing where to deposit metabolomics data to satisfy a journal or funder mandate, or a research administrator reviewing a data management plan (DMP) that names it as the repository of record, this guide covers what MetaboLights actually is, who runs it, what data types and submission format it requires, and how it relates to Metabolomics Workbench, its U.S. counterpart.
What Is MetaboLights?
MetaboLights is a global, cross-species, cross-technique database for metabolomics experiments and the metadata associated with them, launched in 2012. It is recommended as a deposition repository by a number of major journals and is part of ELIXIR, Europe’s distributed life-science data infrastructure. Like other established domain repositories, MetaboLights is not a simple file-drop archive: every submitted study is expected to carry structured, machine-readable experimental metadata alongside the measurement data itself, so that a dataset remains interpretable and reusable once it leaves the lab that produced it. That positions it, in the vocabulary CASRAI uses elsewhere on this site, as a discipline-specific repository built around the conventions a specific measurement community actually produces.
Who Runs and Funds MetaboLights
MetaboLights is hosted and operated by the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), based at the Wellcome Genome Campus in Hinxton, UK, and is part of ELIXIR, the pan-European consortium that coordinates life-science data resources across member states. Funding for the resource has drawn on multiple sources over its history, including the Wellcome Trust, EU Horizon 2020 programmes, the UK Medical Research Council, the UK Biotechnology and Biological Sciences Research Council, and the U.S. National Institute of Environmental Health Sciences, reflecting the mixed European/international funding base typical of EMBL-EBI’s major data resources.
What Data Types MetaboLights Hosts
MetaboLights accepts metabolomics data from both major analytical approaches used in the field: mass spectrometry (MS), including liquid chromatography-MS, gas chromatography-MS, and direct-infusion methods, and nuclear magnetic resonance (NMR) spectroscopy. It covers both targeted studies (quantifying a defined panel of known metabolites) and untargeted studies (broad, exploratory profiling without a predefined target list), and spans a wide range of source organisms, with human, mouse, and Arabidopsis thaliana among the most heavily represented in the archive. As with any domain repository, the practical scope question for a submitter is whether a given dataset is genuinely a metabolomics study in this sense, rather than, for example, raw untyped chromatography output with no accompanying experimental design.
Submission Requirements: the ISA Framework and ISA-Tab
MetaboLights submissions are built on the ISA (Investigation-Study-Assay) model, a general-purpose framework and toolset for reporting and managing experimental metadata, covering sample characteristics, the technology and measurement types used, and the relationships between samples and the resulting data files. Metadata is captured in ISA-Tab format, a tabular, structured representation of that Investigation-Study-Assay structure, rather than as free-text description. This is a materially different submission format from Metabolomics Workbench’s own mwTab standard; the two repositories have collaborated on interoperability work, including tested workflows for moving specific studies between systems, but do not currently share a single common submission format, so metadata prepared for one is not automatically usable by the other without conversion.
During curation, MetaboLights’ curation team works to standardize the metabolite names reported in a submission by mapping them to ChEBI (Chemical Entities of Biological Interest) identifiers, work that supports downstream interoperability with other biological databases and aligns with the FAIR data principles the repository states as a design goal. Submitters should expect this curation step, rather than automatic, unreviewed publication, between deposit and public release.
Accession Numbers: MTBLS IDs and the Submission Workflow
A completed MetaboLights study is assigned a persistent study identifier in the format MTBLS followed by a number (for example, MTBLS718). Per MetaboLights’ own submission documentation, newer submissions first receive a temporary submission reference (in a REQ-prefixed format) at the point of initial upload, with a full MTBLS accession number assigned only once the study has passed the repository’s Validation Framework checks. A research administrator checking a closeout report or DMP compliance record against a stated MetaboLights deposit should confirm the citation is a finalized MTBLS accession, not a placeholder submission reference, since only the former is a stable, citable identifier.
MetaboLights vs. Metabolomics Workbench
MetaboLights and Metabolomics Workbench are the two major general-purpose metabolomics data repositories, and are widely described in the field as complementary, geographically distinct counterparts: MetaboLights operated by EMBL-EBI in Europe as part of ELIXIR, Metabolomics Workbench operated by the U.S. National Metabolomics Data Repository under the NIH Common Fund. The comparison is loosely analogous to how the European Nucleotide Archive and NCBI’s Sequence Read Archive both serve as regional points of deposit for sequencing data. The two repositories are independent systems, not a single shared database, and use different metadata formats (ISA-Tab for MetaboLights, mwTab for Metabolomics Workbench), but they have worked together on interoperability, including collaboration on shared or convertible flat-file exchange approaches and tested cross-repository workflows. For a submitter, the practical implication is the same as with any pair of regionally distinct repositories: check the specific journal’s or funder’s data-deposition policy before choosing between them. Some policies accept either, some name one specifically (European funders and journals more often point to MetaboLights, U.S. NIH-funded studies more often point to Metabolomics Workbench), and a small number of studies are deposited in both to satisfy overlapping requirements.
Why This Matters for Research Administration
For a research administrator reviewing a data management plan that names MetaboLights as the repository of record, the checks worth running mirror those for any named domain repository: does the study’s data type genuinely fall within MetaboLights’ accepted scope (MS or NMR metabolomics data, with structured ISA-Tab metadata, not just raw instrument output); does the plan account for the metadata-preparation burden of ISA-Tab submission, which is a hard requirement rather than optional context; and, once deposited, is the finalized MTBLS accession number (not a temporary REQ reference) recorded in the award’s closeout documentation as evidence the data-sharing commitment was actually met. Because ELIXIR resources like MetaboLights are grant- and consortium-funded rather than commercially operated, they generally don’t carry CoreTrustSeal-style certification fees, but a DMP reviewer can still check a repository’s certification and preservation commitments via resources like the re3data registry before accepting it as adequate for a funder’s data-sharing requirement.
Frequently Asked Questions
Is MetaboLights free to use?
Yes. MetaboLights is a public, open-access repository; there is no charge to deposit or to access public studies.
What is an MTBLS accession number?
It is the persistent identifier MetaboLights assigns to a completed, validated study, in the format MTBLS followed by a number. It is issued once a submission has passed the repository’s validation checks, not at the moment of initial upload.
Is MetaboLights the same organization as Metabolomics Workbench?
No. They are independently operated repositories, MetaboLights by EMBL-EBI/ELIXIR in Europe and Metabolomics Workbench by the U.S. NIH Common Fund’s National Metabolomics Data Repository. They are commonly described as complementary regional counterparts and have collaborated on interoperability, but they are separate systems with separate submission formats.
What metadata format does MetaboLights require?
Submissions use the ISA (Investigation-Study-Assay) framework, with metadata captured in ISA-Tab format. This is distinct from the mwTab format used by Metabolomics Workbench.
What data types can be deposited in MetaboLights?
Mass spectrometry data (including LC-MS, GC-MS, and direct-infusion methods) and NMR spectroscopy data, covering both targeted and untargeted metabolomics studies across a wide range of source organisms.
