SMDB's simple text query (TextQuery) supports general text queries including names, synonyms, conditions and disorders. Clicking on the Browse button (on the SMDB navigation panel) generates a tabular view that allows users to casually scroll through the database or re-sort its contents by compound name or by concentration. Users can choose either the “Metabolite View” or “Associated Condition View” to facilitate their browsing or searching. Clicking on a given MetaboCard button brings up the full data content (from the HMDB) for the corresponding metabolite. The ChemQuery button allows users to draw or write (using a SMILES string) a chemical compound to search the SMDB for chemicals similar or identical to the query compound. ChemQuery also supports chemical formula and molecular weight searches. 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 protein 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 in SMDB. SMDB's 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 potentially allows facile identification of serum metabolites from mixtures via MS/MS spectroscopy. SMDB's NMR Search allows users to submit peak lists from 1 H or 13 C 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 Explain button lists source data used to assemble the SMDB.
Depending on the sample type and platform, 10-30% of all detectable peaks are identified by retention times and mass spectra from MassBank of North America , yielding additional hundreds of structurally unknown compounds for discovery work. Quantitative data are typically reported as relative peak intensities (for example, normalized to the peak intensities found in quality control samples).
Targeted analyses screen only for sets of defined, carefully selected metabolites with high importance in specific biological matrices. Targeted assays perform absolute quantification using sets of stable isotope labeled internal standards. Usually, targeted assays are performed on low abundant compounds that are not detected by discovery-driven untargeted analyses.