Part 1. Introduction -- 1. Introduction -- Part 2. From Sample Collection to Data Acquisition 2. Sample collection and handling: practices to follow -- 3. How to prepare your samples for polar metabolite analysis? -- 4. How to extract lipid metabolites and perform lipid analysis? -- Part 3. From Data Processing to Polar and Lipid Metabolite Identification 5. Data processing & metabolite annotation using XCMS-METLIN -- 6. GC/MS data processing and metabolite identification -- Part 4. From Statistical Data Analysis to Insights into Biology 7. Workflow for knowledge discovery from metabolomic data using chemometrics -- 8. Using Quantitative Metabolomics and Data Enrichment to Interpret the Biochemistry of a Novel Disease -- Part 5. Metabolomics to Decipher Physiology in Health and Disease: Clinical Research Studies 9. Automated sample preparation for blood plasma lipidomics -- 10. NMR based Metabolomics in the context of exercise -- 11. Identifying sex-specific cancer metabolites and associations to prognosis -- 12. A lipidome-wide association study: Data processing, annotation and analysis workflow using MS-DIAL and R -- 13. Quantitative analysis of eicosanoids and other oxylipins - Investigation of oxidative stress and inflammation by means of targeted metabolomics of oxylipins in cell culture -- Part 6. Spatial Metabolite Analysis using MS-assisted Tissue Imaging 14. Spatial lipidomics on and off-tissue analysis -- 15. Spatial isotopic tracing -- 16. Quantitative imaging using SIMS.