Comparison between the coverage in HMDB 1.0, 2.0, 3.0 and HMDB 4.0
| Category | HMDB 1.0 | HMDB 4.0 |
|---|---|---|
| Total number of metabolites | 2180 | 114 100 |
| Number of detected & quantified metabolites | 883 | 18 557 |
| Number of detected, not quantified metabolites | 1297 | 3271 |
| Number of expected metabolites | 0 | 82 274 |
How many metabolites are in the human metabolome?
Metabolite Statistics
| Description | Count |
|---|---|
| Total Number of Cosmetic Metabolites | 17 |
| Total Number of Metabolites Having Associated Proteins (Enzymes and Transporters) | 21,645 |
| Total Number of Metabolite in the Human Metabolome Library (HML) | 867 |
| Total Number of Metabolites with Synthesis Records | 1,608 |
Which is a metabolomic database?
The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases.
What is first metabolite database?
One of the first dedicated metabolomics databases, the HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. …
What are human metabolites?
Metabolites are the intermediate products of metabolic reactions catalyzed by various enzymes that naturally occur within cells. This term is usually used to describe small molecules, although broader application is often practiced.
What is a metabolite metabolome?
Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome.
What metabolites are in urine?
The least abundant (detectable) metabolites in urine include oxytocin (0.9 ± 0.1 pM/mM creatinine), angiotensin II (1.2 ± 0.2 pM/mM creatinine), 15-deoxy-d-12,14-PGJ2 (2.3 ± 1.0 pM/mM creatinine) and melatonin (3.3 ± 2.7 pM/mM creatinine).
What do you mean by metabolite?
Listen to pronunciation. (meh-TA-boh-lite) A substance made or used when the body breaks down food, drugs or chemicals, or its own tissue (for example, fat or muscle tissue). This process, called metabolism, makes energy and the materials needed for growth, reproduction, and maintaining health.
How do you reference a human metabolome database?
Please cite: Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. 17202168.
What is the difference between proteomics and metabolomics?
The key difference between proteomics and metabolomics is that proteomics is the study of all proteins of an organism while metabolomics is the study of all metabolites of an organism. Genomics is the study of the genetic make-up of an organism.
How big is the metabolome?
1.5 kDa
The metabolome refers to the complete set of small-molecule (<1.5 kDa) metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism.
How was the Human Metabolome library developed?
The Human Metabolome Library has been developed through the efforts of the Human Metabolome Project. Each of the HML’s 1020 in-stock compounds were acquired through purchase, custom synthesis or purification. Researchers interested in HML may contact The Metabolomics Innovation Centre for further information.
How many metabolites are there in the database?
The database contains 106,191 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, 5,702 protein sequences are linked to these metabolite entries.
How can I obtain metabolites from the HML for research purposes?
Researchers may obtain metabolites from the HML for basic research purposes by contacting The Metabolomics Innovation Centre (TMIC). Available compounds are provided in amounts of ~10mg each, with the Metabolomics Innovation Centre acknowledged in any resulting publications or presentations.
How many data fields are in a MetaboCard?
Each MetaboCard entry contains 130 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases ( KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank) and a variety of structure and pathway viewing applets.
