Metabolomics is the scientific study of the chemical processes in a living system, environment and nutrition. It is a relatively new omics science, but the potential applications are wide, including medicine, personalized medicine and intervention studies, food and nutrition, plants, agriculture and environmental science. The topics presented and discussed in this book are based on the European Molecular Biology Organization (EMBO) practical courses in metabolomics bioinformatics taught to those working in the field, from masters to postgraduate students, PhDs, postdoctoral and early PIs. The book covers the basics and fundamentals of data acquisition and analytical technologies, but the primary focus is data handling and data analysis. The mentioning and usage of a particular data analysis tool has been avoided; rather, the focus is on the concepts and principles of data processing and analysis. The material has been class-tested and includes lots of examples, computing and exercises.
- Provides an overview of qualitative /quantitative methods in metabolomics
- Offers an introduction to the key concepts of metabolomics, including experimental design and technology
- Covers data handling, processing, analysis, data standards and sharing
- Contains lots of examples to illustrate the topics
- Includes contributions from some of the leading researchers in the field of metabolomics with extensive teaching experiences
Ron Wehrens was an associate professor at the Radboud University Nijmegen (Netherlands) before founding the Biostatistics unit at the Fondazione Edmund Mach, San Michele all'Adige (Italy). Currently, he is Business Unit Manager at Biometris, Wageningen University & Research, Netherlands.
Reza Salek* has worked in the past in the University of Cambridge and The European Molecular Biology Laboratory European Bioinformatics Institute (EMBL EBI), Cambridge UK. He is currently scientist at The International Agency for Research on Cancer, an intergovernmental agency forming part of the World Health Organization of the United Nations, Lyon France.
*Where authors are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / World Health Organization
Overview of Metabolomics - Oscar Yanes, Reza Salek, Igor Marin, Marta Cascante
Study Design and Preparation - Pietro Franceschi, Oscar Yanes and Ron Wehrens
Measurement Technologies - Oscar Yanes, Katherine Hollywood, Roland Mumm, Maria Vinaixa, Naomi Rankin, Ron Wehrens and Reza Salek
Mass Spectrometry Data Processing - Steffen Neumann, Oscar Yanes, Roland Mumm, Pietro Franceschi
Nuclear Magnetic Resonance Spectroscopy Data Processing - Maria Vinaixa, Naomi Rankin, Jeremy Everett and Reza Salek
Statistics: the essentials - Ron Wehrens and Pietro Franceschi
Data fusion in metabolomics - Johan A. Westerhuis, Frans van der Kloet, Age K. Smilde
Genome-scale metabolic networks - Clément Frainay & Fabien Jourdan
Metabolic flux - Igor Marín de Mas and Marta Cascante
Data Sharing and Standards
Appendix: Metabolic and transcriptional response of Arabidopsis thaliana wildtype and mutants to Phytophthora infestans - Tilo Lübken, Michaela Kopischke, Kathrin Geissler, Lore Westphal, Dierk Scheel, Steffen Neumann, Sabine Rosahl