This chapter describes the open-source tool suite OpenMS. OpenMS contains more than 180 tools which can be combined to build complex and flexible data-processing workflows. The broad range of functionality and the interoperability of these tools enable complex, complete, and reproducible data analysis workflows in computational proteomics and metabolomics. We introduce the key concepts of OpenMS and illustrate its capabilities with a complete workflow for the analysis of untargeted metabolomics data, including metabolite quantification and identification.
Keywords: Data analysis; Metabolomics; OpenMS; Reproducible science; Workflows.