Skip to main content
BioData Science Initiative

MetaboBank

Last updated 2026/06/29Edit

DDBJ's public metabolomics repository, accepting metabolome data from MS, NMR, and mass spectrometry imaging with metabolite assignments in MAGE-TAB format.

About MetaboBank

MetaboBank is a public metabolomics data repository operated by DDBJ. It accepts metabolome data acquired by mass spectrometry (MS), NMR, and mass spectrometry imaging (MSI), together with metabolite assignments.

Metadata uses the MAGE-TAB format, the same family as GEA, and is compatible with the ISA-TAB format used by MetaboLights at EBI. MetaboBank and MetaboLights cooperate in data standardization.

NOTE

For an overview of service selection and submission steps, see the Submit Navigator. MetaboBank submissions proceed as individually-handled cases coordinated through an application form.

Accepted data

The supported measurement modalities and file types are as follows.

CategoryContents
MSLC-MS / LC-DAD-MS / GC-MS / GCxGC-MS / GC-FID-MS / CE-MS / DI-MS / FIA-MS / MALDI-MS
MSIMass spectrometry imaging (image data and instrument information)
NMRNMR measurement data (bundling the instrument configuration file is recommended)

Files fall into one of three types.

TypeContents
Raw dataNative output from the instrument. For MS, open formats such as mzML are accepted as raw; for NMR, formats such as nmrML are accepted as raw
Processed dataAnalysed data and summaries, referenced from columns in the SDRF
MAF (Metabolite Assignment File)Standard TSV table of identified or putative compounds. Separate templates are provided for MS and NMR. Strongly recommended

File names may use only alphanumerics, _, -, and ., and must be unique within a Study. Files can be bundled per Study and uploaded as tar or zip archives. On release, raw data are also provided in Reifycs' mzB format and can be browsed with the dedicated viewer DataChaker.

WARNING

Before uploading, remove any information embedded in raw data files that could lead back to individuals, such as local file paths. For human-derived samples, direct identifiers must also be removed from the metadata.

Accession numbers

The following accession numbers are issued for a MetaboBank Study and its associated BioProject / BioSample records.

TargetFormatExample
MetaboBank StudyMTBKS####MTBKS1234
BioProjectPRJDB######PRJDB123456
BioSample (Omics package)SAMD########SAMD00012345

Data are typically cited as a set of MTBKS#### + PRJDB###### + SAMD########.

Submission flow

  1. Obtain a DDBJ account and register your public key (for scp / sftp).
  2. Apply for submission via the MetaboBank registration application form.
  3. Register a BioProject to obtain a PRJDB######.
  4. Register each sample via the BioSample Omics package to obtain SAMD##### accessions.
  5. Fill in IDF + SDRF in the MAGE-TAB Excel template that matches your measurement type, and prepare a MAF if applicable.
  6. Compute MD5 checksums and prepare a file list for the raw data, processed data, and MAF.
  7. Upload files to the file server via scp / sftp (tar / zip archives per Study are recommended).
  8. The MetaboBank team reviews the contents and issues an MTBKS#.
  9. Decide the release setting (immediate release, or hold until publication).

IMPORTANT

Unlike the self-service web forms used by DRA or GEA, MetaboBank uses an individually-handled workflow that starts from an application form and is coordinated with the MetaboBank team.

Prerequisites (MAGE-TAB and MAF)

Prepare the following before applying:

  • A DDBJ account, with a public key registered for scp / sftp.
  • A BioProject (PRJDB) and BioSample Omics package (SAMD) records.
  • The MAGE-TAB Excel template (IDF + SDRF) for your measurement type.
  • A MAF template (MS or NMR) if applicable.
  • File list and MD5 checksums.

MAGE-TAB (IDF + SDRF)

  • IDF (Investigation Description Format): Captures the Study overview, experimental design, protocols, and publication information.
  • SDRF (Sample and Data Relationship Format): Describes the relationships between samples, assays, and data files as a natural workflow.

Dedicated templates are provided per measurement type (LC-MS / LC-DAD-MS / GC-MS / GCxGC-MS / GC-FID-MS / CE-MS / DI-MS / FIA-MS / MALDI-MS / MSI / NMR).

MAF (Metabolite Assignment File)

A standard TSV table describing identified or putative compounds. Separate Excel templates are provided for MS and NMR. Representative fields include:

FieldContents
ChEBI IDCompound identifier
Formula / SMILES / InChIStructural information
Retention time / chemical shiftMS / NMR measurement parameters
MSI confidence scoreAssignment confidence for MSI
maf_value_unitUnit such as peak area or concentration

MSI (mass spectrometry imaging)

A dedicated metadata template is provided for MSI, capturing image data together with instrument information and acquisition conditions. Assignments are described in the MAF using MSI-specific confidence scores.

Relationship with MetaboLights

MetaboBank's MAGE-TAB format is compatible with the ISA-TAB format used by MetaboLights at EBI. The two repositories cooperate in data standardization, and the metadata format belongs to the same MAGE-TAB family as GEA (ArrayExpress lineage) and SDRF-Proteomics.

NOTE

According to the official documentation, public MetaboBank data are not currently exchanged with EBI MetaboLights.

Release policy

  • Immediate release, or hold (embargo) until publication, can be selected.
  • The release date can be set up to three years ahead, and may be extended.
  • Release follows the DDBJ data release policy, and aligns with the release timing of the linked BioProject / BioSample records.
  • Reviewer access for peer review is arranged with the MetaboBank team and provided via a password-protected site.
  • Post-submission updates are requested through a dedicated form to the MetaboBank team.

Search UI

Released Studies can be browsed and searched from the MetaboBank search UI at https://mb2.ddbj.nig.ac.jp/. Raw data provided in Reifycs' mzB format are viewed with the dedicated viewer DataChaker.