Mass spectral and NMR libraries

MassBank of North America (MoNA)
MoNA provides free MS/MS and GC-MS spectra for > 80,000 compounds from,, LipidBlast, ReSpect, GNPS, HMDB et al.

NIST17 is a licensed mass spectral library, including MS/MS spectra for 14,351 compounds, but also GC-MS spectra of 267,376 unique compounds.


Metlin is a licensed mass spectral library of MS/MS spectra for over 14,000 compounds.


BMRB provides 1D and 2D NMR spectra (time domain and processed) for about 1,000 standard metabolites


Metabolomic data repositories

NIH MetabolomicsWorkbench

This U.S.-based repository contains public data  sets for more than 1,100 metabolomics studies, in addition to protocols, analysis tools and links.

EU MetaboLights

This E.U.-based repository contains public data  sets for more than 300 metabolomics studies, in addition to analysis tools.


Metabolite information and ontology databases

Human Metabolome Database

The free HMDB repository for information on metabolites found in humans, with literature references and concentration values in organs.

Dictionary of Natural Products

The Chapman & Hall CRC database contains information for more than 40,000 natural products.


The free NCBI database contains information for more than 93 million compounds, including REST services and substructure relationships.


The free RSC database contains information for more than 60 million compounds from 480 sources.

Chemical Entities of Biological Interest

The free ChEBI resource is a E.U.-based database and ontology for small molecules, enabling web services.

Medical Subject Headings

The free MeSH system is a controlled vocabulary and ontology system that now classifies more than 85,000 compounds in great detail.


Metabolite pathways and -omics integration databases

Omics discovery index

DataMed is a biomedical data search engine with currently 74 repositories and 2,336,403 datasets.

Kyoto Enzyclopedia of Genes and Genomes (KEGG)

The KEGG databases include enzymes, reactions, glycans and ligands for 10,788 reactions in 521 biochemical pathway maps.


MetaCyc is a free, curated database of 2609 experimentally elucidated metabolic pathways from 2914 different organisms.


Brenda is a free collection of functional data, including reactions and metabolic products and substrates, for more than 6,500 enzymes.


Reactome is a free, open-source, curated biochemical pathway database, e.g., for 11426 reactions in 2179 human metabolic pathways.


Recon2 is a free consensus reconstruction database of  human metabolism from existing resources.