Metabolome Analysis
An Introduction
Wiley-Interscience Series on Mass Spectrometry
1. Edition March 2007
330 Pages, Hardcover
Practical Approach Book
Short Description
This book provides a concise and practical text to introduce students and researchers to metabolome analysis. The book begins with an introduction to the concepts behind metabolomics,discusses metabolites from a chemical standpoint and the analytical challenges that they present, and then moves on to sampling, sample preparation, analytical tools, and data analysis and management. While mass spectrometry is the primary tool for metabolome analysis, it is not on its own a perfect one, and so the authors also discuss liquid and gas chromatography, highlighting the advantages and limitations of each technique. Perhaps the most unique feature of this book is the inclusion of four chapters discussing successful metabolome studies of different organisms.
A concise, interdisciplinary introduction to metabolome analysis
This practical reference focuses on the principles of metabolome analysis and treats metabolomics as a field of its own, rather than as just an additional analytical tool in science. Part I guides readers through the primary steps in metabolite analysis, beginning with an overview of the terminology and the basic concepts of cell metabolism, and the dynamics of biochemical reactions and metabolite turnover. It then discusses the most common methodologies for sample preparation, sample techniques, detection and identification methods, analytical tools (including liquid and gas chromatography as well as mass spectrometry), and data analysis.
Part II illustrates the applicability of metabolomics and discusses specific peculiarities and requirements of metabolomics in certain groups of organisms. It reviews successful cases of metabolome analysis with chapters on:
* Yeast metabolomics
* Specialized sampling devices for microbial metabolomics
* Major achievements in plant metabolomics
* Metabolomics in the classification of filamentous fungi
* Metabolomics applied to humans and other mammals
This is the definitive, core reference on metabolome analysis for research scientists in biochemistry and analytical chemistry, as well as academics, researchers, and technicians in the fields of functional genomics and metabolic engineering. It is also a practical text for scientists working to discover metabolites from natural sources and for graduate students in a variety of courses.
LIST OF CONTRIBUTORS.
PART I: CONCEPTS AND METHODOLOGY.
1 Metabolomics in Functional Genomics and Systems Biology.
1.1 From genomic sequencing to functional genomics.
1.2 Systems biology and metabolic models.
1.3 Metabolomics.
1.4 Future perspectives.
2 The Chemical Challenge of the Metabolome.
2.1 Metabolites and metabolism.
2.2 The structural diversity of metabolites.
2.3 The number of metabolites in a biological system.
2.4 Controlling rates and levels.
2.5 Metabolic channeling or metabolons.
2.6 Metabolites are arranged in networks that are part of a cellular interactome.
3 Sampling and Sample Preparation.
3.1 Introduction.
3.2 Quenching--the fi rst step.
3.3 Obtaining metabolites from biological samples.
3.4 Metabolites in the extracellular medium.
3.5 Improving detection via sample concentration.
4 Analytical Tools.
4.1 Introduction.
4.2 Choosing a methodology.
4.3 Starting point--samples.
4.4 Principles of chromatography.
4.5 Chromatographic systems.
4.6 Mass spectrometry.
4.7 The analytical work-fl ow.
4.8 Data evaluation.
4.9 Beyond the core methods.
4.10 Further reading.
5 Data Analysis.
5.1 Organizing the data.
5.2 Scales of measurement.
5.3 Data structures.
5.4 Preprocessing of data.
5.5 Deconvolution of spectroscopic data.
5.6 Data standardization (normalization).
5.7 Data transformations.
5.8 Similarities and distances between data.
5.9 Clustering techniques.
5.10 Classifi cation techniques.
5.11 Integrated tools for automation, libraries, and data evaluation.
PART II: CASE STUDIES AND REVIEWS.
6 Yeast Metabolomics: The Discovery of New Metabolic Pathways in Saccharomyces cerevisiae.
6.1 Introduction.
6.2 Brief description of the methodology used.
6.3 Early discoveries.
6.4 Yeast stress response gives evidence of alternative pathway for glyoxylate biosynthesis in S. cerevisiae.
6.5 Biosynthesis of glyoxylate from glycine in S. cerevisiae.
7 Microbial Metabolomics: Rapid Sampling Techniques to Investigate Intracellular Metabolite Dynamics--An Overview.
7.1 Introduction.
7.2 Starting with a simple sampling device proposed by Theobald et al. (1993).
7.3 An improved device reported by Lange et al. (2001).
7.4 Sampling tube device by Weuster-Botz (1997).
7.5 Fully automated device by Schaefer et al. (1999).
7.6 The stopped-fl ow technique by Buziol et al. (2002).
7.7 The BioScope: a system for continuous-pulse experiments.
7.8 Conclusions and perspectives.
8 Plant Metabolomics.
8.1 Introduction.
8.2 History of plant metabolomics.
8.3 Plants, their metabolism and metabolomics.
8.4 Specifi c challenges in plant metabolomics.
8.5 Applications of metabolomics approaches in plant research.
8.6 Future perspectives.
9 Mass Profi ling of Fungal Extract from Penicillium Species.
9.1 Introduction.
9.2 Methodology for screening of fungi by DiMS.
9.3 Discussion.
9.4 Conclusion.
10 Metabolomics in Humans and Other Mammals.
10.1 Introduction.
10.2 A brief history of mammalian metabolomics.
10.3 Sample preparation for mammalian metabolomics studies.
10.4 Sample analysis.
10.5 Applications.
10.6 Future outlook.
INDEX.
UTE ROESSNER, PHD, is a Post-Doctoral Fellow at the Australian Centre for Plant Functional Genomics at the University of Melbourne, Australia.?
MICHAEL A. E. HANSEN, PHD, is a Post-Doctoral Fellow at BioCentrum-DTU, Technical University of Denmark.
JØRN SMEDSGAARD, PHD, is an Associate Professor at the Center for Microbial Biotechnology, BioCentrum-DTU?at the Technical University of Denmark.
JENS NIELSEN, PROFESSOR, Dr. techn., PHD, is the Director of the Center for Microbial Biotechnology at the Technical University of Denmark.
