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HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see below). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.

How to cite the HMDB database.

Protein/Gene Sequences (in FASTA Format)

Data SetProtein SequencesGene Sequences
All Metabolite Metabolizing Enzymes

Structures (in SDF Format)

Data SetSDF File
Metabolite Structures Download

Flat Files (in MetaboCard Format)

Data SetMetaboCard File
All Metabolites Download

Spectra

Data SetMetaboCard File
Mass Spectra Image Files Download
GC-MS Peak Lists Download
NMR Spectra FIDS Files Download
NMR Spectra Peaklist Files Download
13C NMR and 1H Download
Mass Spectra and NMR Spectra Files in HTML format Download

Protein/Gene Sequences (in FASTA Format)

Data SetProtein SequencesGene Sequences
All Metabolite Metabolizing Enzymes Download Download

Structures (in SDF Format)

Data SetSDF File
Metabolite Structures Download

Flat Files (in MetaboCard Format)

Data SetMetaboCard File
All Metabolites Download

Spectra

Data SetMetaboCard File
Mass Spectra Image Files Download
GC-MS Peak Lists Download
NMR Spectra FIDS Files Download
NMR Spectra Peaklist Files Download
13C NMR and 1H Download
Mass Spectra and NMR Spectra Files in HTML format Download

Protein/Gene Sequences (in FASTA Format)

Data SetReleased onProtein SequencesGene Sequences
All Metabolite Metabolizing Enzymes2017-09-10 Download Download

Structures (in SDF Format)

Data SetReleased onSDF File
Metabolite Structures2017-09-10 Download

Metabolite and Protein Data (in XML format)

Data SetReleased onXML File
All Metabolites2017-08-27 Download
All Proteins2017-09-10 Download
Urine Metabolites2017-09-10 Download
Serum Metabolites2017-08-13 Download
CSF Metabolites2017-09-10 Download
Saliva Metabolites2017-09-10 Download
Feces Metabolites2017-09-10 Download
Sweat Metabolites2017-09-10 Download

Spectra

Data SetReleased onDownload Link
Mass Spectra Image Files2014-11-17 Download
GC-MS Peak Lists2014-11-17 Download
NMR Spectra FIDS Files2014-11-17 Download
NMR Spectra Peaklist Files2014-11-17 Download
Spectra information (in XML format)2014-11-17 Download

Protein/Gene Sequences (in FASTA Format)

Data SetReleased onProtein SequencesGene Sequences
All Metabolite Metabolizing Enzymes2018-07-09 Download | 1.87 MB Download | 2.88 MB

Structures (in SDF Format)

Data SetReleased onSDF FileFile Size
Metabolite Structures2018-07-09 Download46.3 MB

Metabolite and Protein Data (in XML format)

Data SetReleased onXML FileFile Size
All Metabolites2018-09-29 Download615 MB
All Proteins2018-07-08 Download26.7 MB
Urine Metabolites2018-07-09 Download26.2 MB
Serum Metabolites2018-07-09 Download197 MB
CSF Metabolites2018-07-09 Download8.23 MB
Saliva Metabolites2018-07-09 Download16.1 MB
Feces Metabolites2018-07-09 Download61.8 MB
Sweat Metabolites2018-07-09 Download3.12 MB

Spectra

Data SetReleased onDownload LinkFile Size
Mass Spectra Image Files2018-12-01 Download166 MB
NMR Spectra FID Files2018-12-01 Download1.92 GB
Raw NMR Spectra Peaklist Files (TXT)2018-12-01 Download918 KB
Raw GC-MS Spectra Peaklist Files (TXT) - Predicted2018-12-01 Download23 MB
Raw MS-MS Spectra Peaklist Files (TXT) - Predicted2018-12-01 Download158 MB
Raw MS-MS Spectra Peaklist Files (TXT) - Experimental2018-12-01 Download2.28 MB
All Raw Spectra Peaklist Files (TXT)2018-12-01 Download1.68 GB
NMR Spectra Files (XML)2018-12-01 Download4.46 MB
GC-MS Spectra Files (XML) - Predicted2018-12-01 Download69 MB
GC-MS Spectra Files (XML) - Experimental2018-12-01 Download17.1 MB
MS-MS Spectra Files (XML) - Predicted2018-12-01 Download485 MB
MS-MS Spectra Files (XML) - Experimental2018-12-01 Download38.1 MB
All Spectra Files (XML)2018-12-01 Download4.1 GB