Small molecule metabolite profiling holds great promise for enabling advances in disease biomarker discovery, enzymatic activity studies, drug promiscuity assays, and basic understanding of metabolic processes. Recent developments in analogous high-throughput biological experiments measuring gene and protein expression have required concomitant advances in computational resources. Following that model, we have created METLIN, a public, web-based data management system to assist a broad array of metabolite research. METLIN catalogues a diverse collection of spectroscopic and chemical data. Included in the database, liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) have demonstrated sufficient resolution and granularity to quantify metabolites on a global scale. Electrospray ionization (ESI) has proven particularly effective in reproducibly ionizing metabolites from a variety of biofluids. Also present, high-resolution FTMS spectra from reference biological samples aid metabolite identification through accurate mass measurement and theoretical isotopic pattern evaluation. Lastly, METLIN includes an annotated list of known metabolite structural information, easily cross-correlated with the LC-MS, GC-MS, and FTMS data. We provide a number of data visualization tools including colorized 3-dimensional LC-MS plots and histograms. METLIN is continually growing in both range and scope and is available on the web at http://metlin.scripps.edu.