Metabolome Analysis An Introduction

Providing information on the main approaches for the analysis of metabolites, this textbook: Covers basic methodologies in sample preparation and separation techniques, as well as the most recent techniques of mass spectrometry. Differentiates between primary and secondary metabolites. Includes four chapters discussing successful metabolome studies of different organisms. Highlights the analytical challenges of studying metabolites. Illustrates applications of metabolome analysis through the use of case studies.

SILAS G. VILLAS-BÔAS, PHD, is a Research Scientist at AgResearch Limited in New Zealand.

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.

Preface
List of Contributors
Concepts and Methodology
Metabolomics in Functional Genomics and Systems Biology
From genomic sequencing to functional genomics
Systems biology and metabolic models
Metabolomics
Future perspectives
The Chemical Challenge of the Metabolome
Metabolites and metabolism
The structural diversity of metabolites
The chemical and physical properties
Metabolite abundance
Primary and secondary metabolism
The number of metabolites in a biological system
Controlling rates and levels
Control by substrate level
Feedback and feedforward control
Control by "pathway independent" regulatory molecules
Allosteric control
Control by compartmentalization
The dynamics of the metabolism-the mass fl ow
Control by hormones
Metabolic channeling or metabolons
Metabolites are arranged in networks that are part of a cellular interactome
Sampling and Sample Preparation
Introduction
Quenching-the fi rst step
Overview on metabolite turnover
Different methods for quenching
Quenching microbial and cell cultures
Quenching plant and animal tissues
Obtaining metabolites from biological samples
Release of intracellular metabolites
Structure of the cell envelopes-the main barrier to be broken
Cell disruption methods
Nonmechanical disruption of cell envelopes
Mechanical disruption of cell envelopes
Metabolites in the extracellular medium
Metabolites in solution
Metabolites in the gas phase
Improving detection via sample concentration
Analytical Tools
Introduction
Choosing a methodology
Starting point-samples
Principles of chromatography
Basics of chromatography
The chromatogram and terms in chromatography
Chromatographic systems
Gas chromatography
HPLC systems
Mass spectrometry
The mass spectrometer-an overview
GC-MS-the EI ion source
LC-MS-the ESI ion source
Mass analyzer-the quadrupole
Mass analyzer-the ion-trap
Mass analyzer-the time-of-fl ight
Detection and computing in MS
The analytical work-fl ow
Separation by chromatography
Mass spectrometry
General analytical considerations
Data evaluation
Structure of data
The chromatographic separation
Mass spectral data
Exporting data for processing
Beyond the core methods
Developments in chromatography
Capillary electrophoresis
Tandem MS and advanced scanning techniques
NMR spectrometry
Further reading
Data Analysis
Organizing the data
Scales of measurement
Qualitative data
Quantitative data
Data structures
Preprocessing of data
Calibration of data
Combining profi le scans
Filtering
Centroid calculation
Internal mass scale correction
Binning
Baseline correction
Chromatographic profi le matching
Deconvolution of spectroscopic data
Data standardization (normalization)
Data transformations
Principal component analysis
Fisher discriminant analysis

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Metabolome Analysis An Introduction

Summary

Author Biography

Table of Contents

Supplemental Materials