MetaboAnalyst is a widely used, comprehensive, web-based tool for metabolomic data processing, data visualization, data interpretation, and data integration. Because of its easy accessibility, interactivity and user-friendliness MetaboAnalyst has become one of the most popular software tools in the field of metabolomics. This chapter provides a brief introduction to the latest version of the MetaboAnalyst web server along with some of the most frequently used modules for MS-based metabolomic analysis. In particular, four MetaboAnalyst modules are described, in detail, including: (1) the Statistical Analysis module, (2) the Enrichment Analysis module, (3) the Pathway Analysis module and (4) the MS-Peaks-to-Pathways module. In addition to describing how the modules can be run and what they do, this chapter also describes the data formats and data requirements for each module. Readers of this chapter should be able to gain a good understanding of the statistical methods and data visualization techniques commonly used in metabolomics and the typical workflows needed to analyze MS-based metabolomic data. It is also hoped that interested readers will be drawn to explore MetaboAnalyst on their own and to discover many of the other rich data analysis offerings accessible through this freely available server.