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. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca.

Three major oxidation products of 2'-deoxycytidine (dC)--5-hydroxy-2'-deoxycytidine (oh5dC), 5-hydroxy-2'-deoxyuridine (oh5dU), and 5,6-dihydroxy-5,6-dihydro-2'-deoxyuridine (dUg)--were analyzed from enzymatically hydrolyzed DNA with reversed-phase high-performance liquid chromatography coupled to electrochemical detection. oh5dC and oh5dU can be detected with high sensitivity (50 fmol) and selectivity (0-0.2 V) from hydrolyzed DNA. dUg is not electrochemically active but can be measured by dehydrating it into oh5dU. The quantities of oh5dC, dUg, and oh5dU in untreated commercial-grade calf thymus DNA are 10, 10, and 0.75 fmol/micrograms of DNA, respectively. These levels increased substantially when calf thymus DNA was exposed to ionizing radiation, H2O2 alone, H2O2 and combinations of Fe3+ or Cu2+ and ascorbate, near-UV light (365 nm), near-UV light in the presence of menadione, and OsO4, indicating that oh5dC, oh5dU, and dUg are major oxidative DNA damage products. The steady-state levels of these products were determined from freshly extracted rat tissues and ranged from less than 0.5 fmol/micrograms of DNA for oh5dU to about 10 fmol/micrograms of DNA for oh5dC and dUg in liver and kidney and 22 fmol/micrograms of DNA for oh5dC in brain. The levels of oxo8dG were also determined and in general were somewhat lower than the levels of oh5dC. These findings reinforce the link between DNA damage induced by oxidative metabolism and spontaneous mutagenesis leading to cancer and aging.