This chapter introduces open source tools for mass spectrometry (MS)-based metabolomics. The tools used include the R language for statistical computing, mzMine and KNIME. A typical MS-metabolomics data set is used for illustration and the tasks of visualisation, peak detection, peak identification, peak collation and basic multivariate data analysis are covered. A discussion of vendor formats and the role of open source software in metabolomics is also included. Example R scripts and KNIME R-nodes are shown, which should enable the reader to apply the principles to their own data.