HMDB Serum Metabolome Toolbox

The Serum Metabolome database (SMDB) is a freely available electronic database containing detailed information about 4651 small molecule metabolites found in human serum along with 10895 concentration values. The data tables may be sorted and searched by concentration values and ranges. The information includes literature and experimentally derived chemical data, clinical data and molecular/biochemistry data. Each MetaboCard entry contains more than 110 data fields and many of them are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank).

The simple text query (TextQuery) supports general text queries of some of the textual component of the database, for example, names, synonyms, cinditions and disorders. Clicking on the Browse button (on the SMDB navigation panel above) generates a browse view that allows users to casually scroll through the database or re-sort its contents by compound common name or by concentration. Users can choose either "Metabolite View" or "Associated Condition View". Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. The ChemQuery button allows users to draw or write (using a SMILES string) a chemical compound to search SMDB for chemicals similar or identical to the query compound. The ChemQuery also allows chemical formula and molecular weight search. The TextQuery button supports a more sophisticated text search (partial word matches, misspellings, etc.) of the text portion of SMDB. The SeqSearch button allows users to conduct BLAST sequence searches of the 6252 sequences contained in SMDB. Both single and multiple sequence BLAST queries are supported. The DataExtractor button opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The DataExtractor is the most sophisticated search tool for SMDB. The MS Search allows users to submit Mass spectral files (MoverZ format) that will be searched against the Human Metabolome database (HMDB)'s library of MS/MS spectra. This allows the identification of metabolites from mixtures via MS/MS spectroscopy. The NMR Search allows users to submit peak lists from 1H or 13C NMR spectra (both pure and mixtures) and to have these peak lists compared to the NMR libraries contained in the HMDB. This allows the identification of metabolites from mixtures via NMR spectroscopy. The Download button provides links to collected sequence, image and text files associated with the SMDB. The HML Home button links to the Human Metabolome Library (HML) home page. The HML lists metabolites that can be ordered for a fee by researchers around the world. The Explain button lists source data used to assemble the SMDB.

SMDB is supported by David Wishart, Departments of Computing Science & Biological Sciences, University of Alberta.

Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B, Young N, Xia J, Knox C, Dong E, Huang P, Hollander Z, Pedersen TL, Smith SR, Bamforth F, Greiner R, McManus B, Newman JW, Goodfriend T, Wishart DS. The human serum metabolome. PLoS One. 2011 Feb 16;6(2):e16957.