Downloads
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.
Protein/Gene Sequences (in FASTA Format)
| Data Set | Protein Sequences | Gene Sequences |
|---|---|---|
| All Metabolite Metabolizing Enzymes | — | — |
Structures (in SDF Format)
| Data Set | SDF File |
|---|---|
| Metabolite Structures | Download |
Flat Files (in MetaboCard Format)
| Data Set | MetaboCard File |
|---|---|
| All Metabolites | Download |
Spectra
| Data Set | MetaboCard 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 Set | Protein Sequences | Gene Sequences |
|---|---|---|
| All Metabolite Metabolizing Enzymes | Download | Download |
Structures (in SDF Format)
| Data Set | SDF File |
|---|---|
| Metabolite Structures | Download |
Flat Files (in MetaboCard Format)
| Data Set | MetaboCard File |
|---|---|
| All Metabolites | Download |
Spectra
| Data Set | MetaboCard 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 Set | Released on | Protein Sequences | Gene Sequences |
|---|---|---|---|
| All Metabolite Metabolizing Enzymes | 2017-09-10 | Download | Download |
Structures (in SDF Format)
| Data Set | Released on | SDF File |
|---|---|---|
| Metabolite Structures | 2017-09-10 | Download |
Metabolite and Protein Data (in XML format)
| Data Set | Released on | XML File |
|---|---|---|
| All Metabolites | 2017-08-27 | Download |
| All Proteins | 2017-09-10 | Download |
| Urine Metabolites | 2017-09-10 | Download |
| Serum Metabolites | 2017-08-13 | Download |
| CSF Metabolites | 2017-09-10 | Download |
| Saliva Metabolites | 2017-09-10 | Download |
| Feces Metabolites | 2017-09-10 | Download |
| Sweat Metabolites | 2017-09-10 | Download |
Spectra
| Data Set | Released on | Download Link |
|---|---|---|
| Mass Spectra Image Files | 2014-11-17 | Download |
| GC-MS Peak Lists | 2014-11-17 | Download |
| NMR Spectra FIDS Files | 2014-11-17 | Download |
| NMR Spectra Peaklist Files | 2014-11-17 | Download |
| Spectra information (in XML format) | 2014-11-17 | Download |
Protein/Gene Sequences (in FASTA Format)
| Data Set | Released on | Protein Sequences | Gene Sequences |
|---|---|---|---|
| All Metabolite Metabolizing Enzymes | 2018-12-18 | Download | 1.87 MB | Download | 2.88 MB |
Structures (in SDF Format)
| Data Set | Released on | SDF File | File Size |
|---|---|---|---|
| Metabolite Structures | 2018-12-18 | Download | 46.3 MB |
Metabolite and Protein Data (in XML format)
| Data Set | Released on | XML File | File Size |
|---|---|---|---|
| All Metabolites | 2018-12-18 | Download | 597 MB |
| All Proteins | 2018-12-18 | Download | 26.7 MB |
| Urine Metabolites | 2018-12-18 | Download | 26.9 MB |
| Serum Metabolites | 2018-12-18 | Download | 192 MB |
| CSF Metabolites | 2018-12-18 | Download | 8.39 MB |
| Saliva Metabolites | 2018-12-18 | Download | 16.4 MB |
| Feces Metabolites | 2018-12-18 | Download | 61.4 MB |
| Sweat Metabolites | 2018-12-18 | Download | 3.24 MB |
Spectra
| Data Set | Released on | Download Link | File Size |
|---|---|---|---|
| Mass Spectra Image Files | 2018-12-18 | Download | 161 MB |
| NMR Spectra FID Files | 2018-12-18 | Download | 1.89 GB |
| Raw NMR Spectra Peaklist Files (TXT) | 2018-12-18 | Download | 903 KB |
| Raw GC-MS Spectra Peaklist Files (TXT) - Predicted | 2018-12-18 | Download | 15 MB |
| Raw MS-MS Spectra Peaklist Files (TXT) - Predicted | 2018-12-18 | Download | 166 MB |
| Raw MS-MS Spectra Peaklist Files (TXT) - Experimental | 2018-12-18 | Download | 3.65 MB |
| All Raw Spectra Peaklist Files (TXT) | 2018-12-18 | Download | 10.7 GB |
| NMR Spectra Files (XML) | 2018-12-18 | Download | 4.28 MB |
| GC-MS Spectra Files (XML) - Predicted | 2018-12-18 | Download | 46.2 MB |
| GC-MS Spectra Files (XML) - Experimental | 2018-12-18 | Download | 16.1 MB |
| MS-MS Spectra Files (XML) - Predicted | 2018-12-18 | Download | 509 MB |
| MS-MS Spectra Files (XML) - Experimental | 2018-12-18 | Download | 43.2 MB |
| All Spectra Files (XML) | 2018-12-18 | Download | 20.8 GB |
Protein/Gene Sequences (in FASTA Format)
| Data Set | Released on | Protein Sequences | Gene Sequences |
|---|---|---|---|
| All Metabolite Metabolizing Enzymes | 2021-11-02 | Download | 1.87 MB | Download | 2.88 MB |
Structures (in SDF Format)
| Data Set | Released on | SDF File | File Size |
|---|---|---|---|
| Metabolite Structures | 2021-11-02 | Download | 92 MB |
Metabolite and Protein Data (in XML format)
| Data Set | Released on | XML File | File Size |
|---|---|---|---|
| All Metabolites | 2021-11-17 | Download | 910 MB |
| All Proteins | 2021-11-09 | Download | 34.7 MB |
| Urine Metabolites | 2021-10-24 | Download | 28.1 MB |
| Serum Metabolites | 2021-10-24 | Download | 202 MB |
| CSF Metabolites | 2021-10-24 | Download | 8.49 MB |
| Saliva Metabolites | 2021-10-24 | Download | 16.5 MB |
| Feces Metabolites | 2021-10-24 | Download | 61.2 MB |
| Sweat Metabolites | 2021-10-24 | Download | 3.27 MB |
Spectra
| Data Set | Released on | Download Link | File Size |
|---|---|---|---|
| Mass Spectra Image Files | 2023-07-01 | Download | 163 MB |
| NMR Spectra FID Files | 2023-07-01 | Download | 1.91 GB |
| Raw NMR Spectra Peaklist Files (TXT) | 2023-07-01 | Download | 915 KB |
| Raw GC-MS Spectra Peaklist Files (TXT) - Predicted | 2023-07-01 | Download | 323 MB |
| Raw MS-MS Spectra Peaklist Files (TXT) - Predicted | 2023-07-01 | Download | 186 MB |
| Raw MS-MS Spectra Peaklist Files (TXT) - Experimental | 2023-07-01 | Download | 14 MB |
| All Raw Spectra Peaklist Files (TXT) | 2023-07-01 | Download | 19.8 GB |
| NMR Spectra Files (XML) | 2023-07-01 | Download | 873 MB |
| GC-MS Spectra Files (XML) - Predicted | 2023-07-01 | Download | 872 MB |
| GC-MS Spectra Files (XML) - Experimental | 2023-07-01 | Download | 16.9 MB |
| MS-MS Spectra Files (XML) - Predicted | 2023-07-01 | Download | 2.03 GB |
| MS-MS Spectra Files (XML) - Experimental | 2023-07-01 | Download | 84.5 MB |
| All Spectra Files (XML) | 2023-07-01 | Download | 42.8 GB |