Metabolome Analysis - Villas-Boas, Silas G

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Auteur(s) : Villas-Boas, Silas G - Nielsen, Jens - Smedsgaard, Jorn - Hansen, Michael A E - Roessner-Tunali, Ute

Editeur : John Wiley & Sons

Langue : Anglais

Parution : 01/02/2007

Format : Moyen, de 350g à 1kg

Nombre de pages : 344.0

Expédition : 606

Dimensions : 24.2 x 16.4 x 2.2

ISBN : 0471743445

Résumé :
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.

...

Biographie:

Preface xiii

List of Contributors xv

Part I: Concepts and Methodology

1 Metabolomics in Functional Genomics and Systems Biology 3

1.1 From genomic sequencing to functional genomics 3

1.2 Systems biology and metabolic models 6

1.3 Metabolomics 8

1.4 Future perspectives 11

2 The Chemical Challenge of the Metabolome 15

2.1 Metabolites and metabolism 15

2.2 The structural diversity of metabolites 18

2.2.1 The chemical and physical properties 18

2.2.2 Metabolite abundance 23

2.2.3 Primary and secondary metabolism 24

2.3 The number of metabolites in a biological system 25

2.4 Controlling rates and levels 26

2.4.1 Control by substrate level 27

2.4.2 Feedback and feedforward control 27

2.4.3 Control by pathway independent regulatory molecules 27

2.4.4 Allosteric control 28

2.4.5 Control by compartmentalization 30

2.4.6 The dynamics of the metabolism-the mass flow 31

2.4.7 Control by hormones 33

2.5 Metabolic channeling or metabolons 33

2.6 Metabolites are arranged in networks that are part of a cellular interactome 35

3 Sampling and Sample Preparation 39

3.1 Introduction 39

3.2 Quenching-the first step 41

3.2.1 Overview on metabolite turnover 41

3.2.2 Different methods for quenching 44

3.2.3 Quenching microbial and cell cultures 44

3.2.4 Quenching plant and animal tissues 50

3.3 Obtaining metabolites from biological samples 52

3.3.1 Release of intracellular metabolites 52

3.3.2 Structure of the cell envelopes-the main barrier to be broken 52

3.3.3 Cell disruption methods 58

3.3.4 Nonmechanical disruption of cell envelopes 59

3.3.5 Mechanical disruption of cell envelopes 66

3.4 Metabolites in the extracellular medium 71

3.4.1 Metabolites in solution 72

3.4.2 Metabolites in the gas phase 75

3.5 Improving detection via sample concentration 76

4 Analytical Tools 83

4.1 Introduction 83

4.2 Choosing a methodology 84

4.3 Starting point-samples 86

4.4 Principles of chromatography 87

4.4.1 Basics of chromatography 87

4.4.2 The chromatogram and terms in chromatography 90

4.5 Chromatographic systems 93

4.5.1 Gas chromatography 94

4.5.2 HPLC systems 102

4.6 Mass spectrometry 106

4.6.1 The mass spectrometer-an overview 107

4.6.2 GC-MS-the EI ion source 109

4.6.3 LC-MS-the ESI ion source 111

4.6.4 Mass analyzer-the quadrupole 115

4.6.5 Mass analyzer-the ion-trap 117

4.6.6 Mass analyzer-the time-of-flight 119

4.6.7 Detection and computing in MS 121

4.7 The analytical work-flow 125

4.7.1 Separation by chromatography 125

4.7.2 Mass spectrometry 128

4.7.3 General analytical considerations 129

4.8 Data evaluation 129

4.8.1 Structure of data 129

4.8.2 The chromatographic separation 132

4.8.3 Mass spectral data 133

4.8.4 Exporting data for processing 135

4.9 Beyond the core methods 136

4.9.1 Developments in chromatography 137

4.9.2 Capillary electrophoresis 139

4.9.3 Tandem MS and advanced scanning techniques 141

4.9.4 NMR spectrometry 143

4.10 Further reading 144

5 Data Analysis 146

5.1 Organizing the data 146

5.2 Scales of measurement 147

5.2.1 Qualitative data 148

5.2.2 Quantitative data 148

5.3 Data structures 148

5.4 Preprocessing of data 150

5.4.1 Calibration of data 150

5.4.2 Combining profile scans 151

5.4.3 Filtering 152

5...

Sommaire:
SILAS G. VILLAS-B?AS, 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.

J?RN 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.