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The metabolome is the complete set of metabolites within a cell, tissue or biological sample at any given time point. That wording comes from the EMBL-EBI metabolomics training course, and it contains the two ideas that matter most for research: the metabolome is a set of small molecules, and it is tied to a moment in time. This guide separates the metabolome from the field that studies it (metabolomics) and from the databases that catalogue known metabolites, then shows how it is measured and where to find reference data for free.
What the metabolome is
A metabolite is a small molecule that takes part in, or is produced by, metabolic reactions. Metabolic pathways divide into anabolic reactions, which build molecules, and catabolic reactions, which break them down. The metabolome is everything those reactions leave present in a given cell, tissue or sample at the time you look.
It sits alongside the other “omes” of systems biology, but it is the one closest to what a cell is doing right now, because metabolite levels change as reactions run.
Metabolome vs metabolomics vs database entries
Three terms are often used as if they meant the same thing. They do not.
| Term | What it refers to | Example of how it is used |
|---|---|---|
| Metabolome | The set of metabolites present in a specific cell, tissue or sample at a specific time | “The metabolome of this plasma sample was profiled.” |
| Metabolomics | The study and measurement of metabolomes | “A metabolomics study compared treated and untreated cells.” |
| Database entries | Records in a reference catalogue of known compounds | The Human Metabolome Database (HMDB) 5.0 grew from 114,100 to 217,920 metabolite entries |
The last row is the one most often misread. HMDB 5.0, described by Wishart and colleagues in Nucleic Acids Research (2022, doi:10.1093/nar/gkab1062), reports 217,920 compound entries. That figure counts records in a catalogue of known human metabolites. It is not the size of any person’s metabolome, and it does not tell you how many metabolites a given experiment will detect. The same paper reports that the database holds many more computed items beyond its annotated entries, such as predicted spectra, so a large number in HMDB is not a count of metabolites.
Why the metabolome is a snapshot
EMBL-EBI describes metabolite concentrations as very dynamic: small molecules are continuously made, broken down and interacting with other molecules and the environment. Current techniques therefore capture only a snapshot of the metabolome under defined conditions.
For study design this has a direct consequence. The time of sampling, the conditions at collection and the handling of the sample all belong to the result, so they need to be recorded and kept consistent across a study. Quality-control samples are the usual way to check that a run is stable; see the CASRAI guide to choosing a mass spectrometry platform and QC samples for metabolomics.
How a metabolome is measured
The two main measurement families are mass spectrometry and nuclear magnetic resonance (NMR). HMDB 5.0 holds reference data for both, including 1,440,324 predicted MS/MS spectra and 312,980 predicted 1H/13C NMR spectra.
- Collect and stabilise the sample under defined, recorded conditions, because the result describes that moment.
- Prepare an extract suited to the metabolite classes you want to see.
- Separate and detect. Mass spectrometry is commonly coupled to a separation step; the CASRAI guides on LC-MS and GC-MS versus LC-MS explain the two couplings, and what a mass spectrometer is covers the detector.
- Match signals to compounds by comparing spectra with reference libraries such as HMDB. Signals that match nothing remain unannotated.
- Deposit the data in a public repository so others can reuse it.
Where to access reference data (free)
Three public resources cover lookup and data sharing. All are accessed through their official websites.
| Resource | Operator | Use | CASRAI guide |
|---|---|---|---|
| HMDB (Human Metabolome Database) | HMDB authors (Wishart et al.) | Look up known human metabolites and their reference spectra | – |
| MetaboLights | EMBL-EBI | Deposit and reuse metabolomics study data | MetaboLights guide |
| Metabolomics Workbench | UCSD, sponsored by the NIH Common Fund | Deposit and reuse metabolomics study data | Metabolomics Workbench guide |
FAQ
What is the metabolome in simple terms?
It is the full collection of small molecules, the metabolites, present in a cell, tissue or sample at one point in time.
Is the metabolome the same as metabolomics?
No. The metabolome is the thing being measured; metabolomics is the discipline that measures and studies it.
Does the metabolome change?
Yes. Metabolite concentrations are very dynamic, so a measurement is a snapshot under the conditions in which the sample was taken.
Does HMDB list the whole human metabolome?
HMDB is a catalogue of known human metabolites, with 217,920 entries in version 5.0. Its entry count is a record count, not a measured metabolome.
Sources
- EMBL-EBI Training, Metabolomics introduction: The metabolome and metabolic reactions (checked 2026-10-29).
- Wishart DS et al. HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Research, 2022. doi:10.1093/nar/gkab1062 (checked 2026-10-29).
- Metabolomics Workbench, home page (checked 2026-10-29).
