Metabolomics in food and nutrition

235 Pages·2013·5.669 MB·English

by  Bart C. Weimer, Carolyn Slupsky

Metabolomics in food and nutrition
© Woodhead Publishing Limited, 2013
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© Woodhead Publishing Limited, 2013
Woodhead Publishing Series in Food Science, Technology and Nutrition:
Number 251
Metabolomics in food
and nutrition
Edited by
Bart C. Weimer and Carolyn Slupsky
© Woodhead Publishing Limited, 2013
Published by Woodhead Publishing Limited,
80 High Street, Sawston, Cambridge CB22 3HJ, UK
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© Woodhead Publishing Limited, 2013
Contents
Contributor contact details .......................................................................... ix
Woodhead Publishing Series in Food Science, Technology
and Nutrition ................................................................................................ xi
Introduction .................................................................................................. xxi
Part I Equipment, methods and data interpretation
in metabolomics ........................................................................... 1
1 Equipment and metabolite identifi cation (ID) strategies for
mass- based metabolomic analysis ...................................................... 3
C. J. Wachsmuth, P. J. Oefner and K. Dettmer, University of
Regensburg, Germany
1.1 Introduction ................................................................................. 3
1.2 Liquid chromatography .............................................................. 5
1.3 Gas chromatography ................................................................... 9
1.4 Mass spectrometry technologies ................................................. 12
1.5 Analytical systems ...................................................................... 15
1.6 Compound identifi cation (ID) approaches .................................. 19
1.7 Databases for tracking and interconnections .............................. 22
1.8 Future trends ............................................................................... 23
1.9 Sources of further information and advice ................................. 24
1.10 Acknowledgments ...................................................................... 24
1.11 References ................................................................................... 25
2 Metabolomics using nuclear magnetic resonance (NMR) ............... 29
J. Sotelo and C. M. Slupsky, University of California, Davis, USA
2.1 Introduction ................................................................................. 29
2.2 Experimental design and preparation ......................................... 30
2.3 Experimental process and analysis ............................................. 34
2.4 Current applications and future trends ........................................ 38
2.5 References ................................................................................... 39
2.6 Appendix: abbreviations ............................................................. 43
© Woodhead Publishing Limited, 2013
vi Contents
3 Statistical methods in metabolomics .................................................. 44
J. R. Stevens, Utah State University, USA
3.1 Introduction ................................................................................. 44
3.2 Exploratory/visual approaches .................................................... 46
3.3 Inferential approaches ................................................................. 51
3.4 Multiple hypothesis testing ......................................................... 55
3.5 Ensemble learning approaches ................................................... 60
3.6 Conclusion .................................................................................. 64
3.7 References ................................................................................... 65
3.8 Appendix: software packages used ............................................. 67
4 Metabolic reconstruction databases and their application to
metabolomics research ........................................................................ 68
P. D. Karp, SRI International, USA
4.1 Introduction ................................................................................. 68
4.2 Overview of Pathway/Genome Database (PGDB)
construction ................................................................................. 70
4.3 Querying PGDBs ........................................................................ 72
4.4 Metabolomics applications ......................................................... 75
4.5 Sources of further information and advice ................................. 77
4.6 Conclusion .................................................................................. 78
4.7 Acknowledgments ...................................................................... 78
4.8 References ................................................................................... 78
Part II Applications of metabolomics in humans, plants
and food ................................................................................ 81
5 Human samples for health assessments ............................................. 83
P. D. Whitfi eld and M. K. Doherty, University of the Highlands
and Islands, UK
5.1 Introduction ................................................................................. 83
5.2 Sample collections and biobanks ................................................ 84
5.3 Variation in metabolite profi les of human biofl uids
and tissues ................................................................................... 89
5.4 Standards for metabolomic studies ............................................. 97
5.5 Conclusions and future trends .................................................... 98
5.6 References ................................................................................... 99
6 Metabolomics in nutrition ................................................................... 106
S. Moco, A. Ross, F.-P. J. Martin, S. Collino, J.-P. Godin, S. Rezzi
and S. Kochhar, Nestlé Research Center, Switzerland
6.1 Introduction ................................................................................. 106
6.2 Epidemiological studies and biomarkers of food intake ............. 108
6.3 Diet and metabolic syndrome ..................................................... 110
© Woodhead Publishing Limited, 2013
Contents vii
6.4 The role of intestinal microbiota in nutrition .............................. 111
6.5 Perspectives in nutrition research ............................................... 113
6.6 Future trends ............................................................................... 117
6.7 References ................................................................................... 118
7 Current methods for the analysis of human milk oligosaccharides
(HMOs) and their novel applications ................................................. 124
L. R. Ruhaak and C. B. Lebrilla, University of California, Davis, USA
7.1 Introduction ................................................................................. 124
7.2 Analysis of human milk oligosaccharides (HMOs) .................... 127
7.3 Applications of HMO analysis ................................................... 137
7.4 Conclusion .................................................................................. 140
7.5 References ................................................................................... 141
7.6 Appendix: abbreviations ............................................................. 146
8 Metabolomic analysis of plants and crops ......................................... 148
T. Frank and K.-H. Engel, Technische Universität München,
Germany
8.1 Introduction ................................................................................. 148
8.2 Metabolomic studies on selected Poaceae species ..................... 153
8.3 Metabolomic studies on selected Solanaceae species ................ 168
8.4 Metabolomic studies on selected Fabaceae species .................... 171
8.5 Metabolomic studies on selected Brassicaceae and
Lamiaceae species ...................................................................... 174
8.6 Plant/crop metabolome databases ............................................... 176
8.7 Future trends ............................................................................... 178
8.8 References ................................................................................... 178
9 Metabolomics for the safety assessment of genetically
modifi ed (GM) crops ............................................................................ 192
D. Stewart, The James Hutton Institute and Heriot-Watt University,
UK and L. V. T. Shepherd, The James Hutton Institute, UK
9.1 Introduction ................................................................................. 192
9.2 Solanaceous crops ....................................................................... 194
9.3 Cereal crops ................................................................................ 201
9.4 Other crops .................................................................................. 206
9.5 Metabolomics as part of a regulatory risk assessment
procedure for the development and evaluation of genetically
modifi ed (GM) crops .................................................................. 208
9.6 Metabolomics and GM food safety: future trends ...................... 211
9.7 Acknowledgements ..................................................................... 211
9.8 References ................................................................................... 212
© Woodhead Publishing Limited, 2013
viii Contents
10 Applications of metabolomics in food science: food composition
and quality, sensory and nutritional attributes ................................. 217
E. Chin and C. M. Slupsky, University of California, Davis, USA
10.1 Introduction ................................................................................. 217
10.2 Metabolomics for compound identifi cation: authentication
and pathogen detection ............................................................... 220
10.3 Metabolomics for predicting sensory attributes ......................... 221
10.4 Metabolomics and food processing and safety ........................... 223
10.5 Conclusion .................................................................................. 226
10.6 References ................................................................................... 227
10.7 Appendix: abbreviations ............................................................. 230
Index ............................................................................................................. 231
© Woodhead Publishing Limited, 2013
Contributor contact details
(* = main contact) C hapter 2
J. Sotelo and C. M. Slupsky*
Editors University of California, Davis
Department of Nutrition and
B. C. Weimer
Department of Food Science and
University of California, Davis
Technology
School of Veterinary Medicine
One Shields Avenue
One Shields Avenue
Davis, CA 95616, USA
Davis, CA 95616, USA
E-mail: [email protected];
E-mail: [email protected]
[email protected]
C. M. Slupsky Chapter 3
University of California, Davis
Department of Nutrition and J. R. Stevens
Department of Food Science and Department of Mathematics and
Technology Statistics
One Shields Avenue Utah State University
Davis, CA 95616, USA 3900 Old Main Hill
Logan, UT 84322-3900, USA
E-mail: [email protected]
E-mail: [email protected]
Chapter 1
Chapter 4
C. J. Wachsmuth, P. J. Oefner and
K. Dettmer* P. D. Karp
Institute of Functional Genomics SRI International
University of Regensburg 3 33 Ravenswood Ave, AE206
Josef-Engert-Str. 9 Menlo Park, CA 94025, USA
93053 Regensburg, Germany
E-mail: [email protected]
E-mail: katja.dettmer@klinik.
uni- regensburg.de
© Woodhead Publishing Limited, 2013