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MetaboLights features

How to submit data

There are two possible ways to submit data into MetaboLights:

Non-Personal vs Personal data

Non-personal data (non-identifiable).

Access to data

Open access.


Possible. A minimum of 28 days from submission to allow for manual curation of the study. A longer period may be selected.

Data licence

All data is governed by the EMBL-EBI’s Terms of use.

Data/Experiments types

  • Mass Spectrometry (MS)
  • NMR spectroscopy


  • Study: title, summary/description, keywords
  • Assay: technique and assay type, both defined by controlled vocabulary. For each assay type a set of specific metadata will be required. Find here the specific metadata for each assay type.
  • Protocol description: sample collection, extraction, chromatography, MS, data transformation, metabolite identification.
  • Experimental control names
  • Sample names
  • Sample details: organism, organism part, variant, custom factors/variable. Controlled vocabulary is provided for each metadata field.
  • Metabolite annotation: database_identifier, chemical_formula, smiles, inchi, metabolite_identification, mass_to_charge, fragmentation, modifications, charge, retention_time, taxid, species, database, database_version, reliability, uri, search_engine search_engine_score, smallmolecule_abundance_sub, smallmolecule_abundance_stdev_sub, smallmolecule_abundance_std_error_sub. Controlled vocabulary is provided for most of the metadata field.


Many ontologies are embedded in the submission form. One of the used ontology is EFO. Additionally, MetaboLights recommends the use of Bioportal to find or resolve any ontologies.

Data documentation

MetaboLights doesn’t allow upload of README file. All relevant information about the data need to be provided in the designated metadata fields.

File format(s)

  • Accepted raw file formats: eg. .raw, .d, .cdf, open source formats (.mzML, .nmrML).
  • Study description (i_MTBLSxxx.txt).
  • Sample information (s_MTBLSxxx.txt).
  • Assay information (a_MTBLSxxx.txt).
  • Metabolite information (m_MTBLSxxx.tsv).

Data volume and costs

No limit for data volume. No costs.

Data quality

MetaboLights submission process includes a validation and a manual curation steps. See here for more details.


Unique accession numbers are minted for every study submitted.

Guide and manual

Quick Start Overview. MetaboLights

Online Study Submission. MetaboLights