Practical Guide to Metabolomics Applications in Health and Disease

Julijana Ivanisevic is a Head of the Metabolomics Unit and a Senior Lecturer at the Faculty of Biology and Medicine, University of Lausanne (UNIL), Switzerland. She joined UNIL in 2015 following her postdoctoral training at the Center for Metabolomics and Mass Spectrometry, the Scripps Research Institute (SD, CA). She received her PhD in chemical biology at the Aix-Marseille University, France, in 2011. As a biologist trained in chemistry and evolving in the field of metabolomics and lipidomics over the past fifteen years, the most prominent aspect of her work constitutes the translation of mass spectrometry data into the biochemically and physiologically relevant information. This aspect of metabolomics, including lipidomics, where chemical composition meets biological function, towards understanding metabolite role in human metabolism and physiology is the focus of Ivanisevic team at UNIL. Ivanisevic team is internationally recognized for the development of innovative analytical solutions for polar and lipid metabolite quantification, and their application to biomedical and clinical research studies in the context of cardiometabolic health. With the aim to advance the health monitoring and the prognosis of cardiometabolic risk, Ivanisevic team applies deep targeted mass spectrometry-based approaches to prospective metabolic phenotyping of Swiss population (CoLaus, Complete Health and Heart cohort), in collaboration with clinicians and statistical geneticists. Dr. Ivanisevic serves as a vice-president of the Swiss Metabolomics Society and a member of editorial boards for Metabolites, Metabolomics and Journal of  Mass Spectrometry and Advances in the Clinical Lab. She is also a member of the Metabolomics Working group within International Federation of Clinical Chemistry and Laboratory Medicine (IFCC).Martin Giera is associate professor and head of the Metabolomics Group at the Leiden University Medical Center (LUMC). After studying pharmaceutical sciences in Heidelberg and Munich, becoming a licensed pharmacist, he obtained his Ph.D. degree from Ludwig-Maximilians Universität München (LMU) in pharmaceutical chemistry and did international postdoctoral training at the VU University Amsterdam. He was an assistant professor at the VU University Amsterdam, visiting scientist at Harvard Medical School and visiting professor at the Scripps research institute. Dr. Giera is an internationally renowned expert in metabolomics, lipidomics, lipid mediator analysis, and bioactivity testing. Dr. Giera has been a DAAD fellow (The German Academic Exchange Service) and was a permanent member and chairman of the interdisciplinary committee of FWO (Flanders Science Foundation). He was Guest Editor for several journals and is on the editorial board of Metabolites (MDPI) and serves on the scientific advisory board of Cell Star Protocols. Dr. Giera is coordinator of the multi-national H2020 ITN consortium ArthritisHeal and track chair at the SLAS 2021 conference. His group is internationally renowned for its work on clinical lipidomics and metabolomics. Next to several national and international collaborations his group also has strong ties to national companies and international partners with Dr. Giera being a consultant to several industry partners.

• 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 toprognosis.- 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.