MetaboAnalyst is a comprehensive, Web-based tool designed for processing, analyzing, and interpreting metabolomic data. It handles most of the common metabolomic data types including compound concentration lists, spectral bin lists, peak lists, and raw MS spectra. In addition to providing a variety of data processing and normalization procedures, MetaboAnalyst supports a number of data-analysis tasks using a range of univariate, multivariate, and machine-learning methods. MetaboAnalyst also offers two newly developed approaches-Metabolite Set Enrichment Analysis (MSEA) and Metabolic Pathway Analysis (MetPA)-for metabolomic data interpretation. MSEA helps detect biologically meaningful metabolite sets that have been enriched in human metabolomic studies, while MetPA allows users to identify any metabolic pathways that have been perturbed. MetaboAnalyst enables facile interactive exploration and visualization of nearly all of its results. At the end of each session, it produces a detailed analysis report with graphical, tabular, and textual output that summarizes each analytical method used and each result generated.