Metabolomics Coming of Age with its Technological Diversity

Series Page

Contributors

Chapter One. High-Resolution ¹H-NMR Spectroscopy and Beyond to Explore Plant Metabolome

1 Introduction

2 NMR Signals: Measurable Properties

3 Metabolomics NMR Fingerprinting for Discriminating Plant Metabolomes

4 Metabolomics NMR Profiling and Spectra Annotation

5 Application of ¹H-NMR Profiling

6 New Challenges for ¹H-NMR Metabolomics

7 Concluding Remarks

References

Chapter Two. Application of LC–MS and LC–NMR Techniques for Secondary Metabolite Identification

1 Introduction

2 Principal Secondary Metabolites in Plants

3 Hyphenated Chromatographic Techniques in Metabolite Identification

4 LC–NMR Techniques

5 Combination of LC–MS and LC–NMR in Metabolite Profiling

6 Conclusion

References

Chapter Three. Fast and Ultrafast Quantitative 2D NMR: Vital Tools for Efficient Metabolomic Approaches

1 Introduction

2 Why Quantitative 2D NMR?

3 Fast Conventional 2D NMR Approaches for Quantitative Analysis of Complex Mixtures

4 Going Faster

5 Conclusion

Acknowledgements

References

Chapter Four. Liquid Chromatography Coupled to Mass Spectrometry-Based Metabolomics and the Concept of Biomarker

1 Introduction

2 LC/MS-Based Metabolomics for Biomarker Discovery

3 Conclusion and Perspectives

Acknowledgements

References

Chapter Five. Potential of Fourier Transform Mass Spectrometry for High-Throughput Metabolomics Analysis

1 Introduction

2 Definition of Some Concepts Used in Mass Spectrometry

3 Principle of Fourier Transform Mass Spectrometers

4 Ion Production for Metabolite Analysis

5 FT-MS Applications for Complex Mixture Analysis

6 Metabolite Identification from HRMS Data

7 Conclusion

Acknowledgements

References

Chapter Six. Exploring Metabolome with GC/MS

1 Introduction

2 Sample Extraction for Metabolomic Analysis

3 GC/MS Profiling

4 Data Processing

5 Quantification

6 Applications

7 Conclusion

References

Chapter Seven. The Lipid World Concept of Plant Lipidomics

Abbreviations

1 Introduction

2 The Diversity of Plant Lipids

3 Lipid Extraction

4 Sample Storage

5 Principles of MS Lipid Analysis

6 Plant Lipid Analyses

7 Conclusion

Acknowledgements

References

Chapter Eight. Isotope Ratio Mass Spectrometry Technique to Follow Plant Metabolism: Principles and Applications of ¹²C/¹³C Isotopes

Abbreviations

1 Stable Isotopes at Natural Abundance

2 Definitions

3 Basics of Photosynthetic ¹²C/¹³C Discrimination

4 Practical Aspects of EA-IRMS Measurements

5 Compound-Specific IRMS Analyses

6 Major Advances in Metabolic Patterns Provided by IRMS Techniques

7 Conclusions and Perspectives

References

Chapter Nine. High-Throughput Biochemical Phenotyping for Plants

1 Introduction

2 Biochemical Phenotyping in Medicine, Agro Industry and Agriculture

3 Solutions for a Microplate Pipeline Dedicated to Plant Biochemical Phenotyping

4 Example of HT Biochemical Screen

5 Concluding Remarks

Acknowledgements

References

Chapter Ten. Two Computational Simplex Approaches to Graphical Highlighting Metabolic Phenotypes and Their Functional Origins: Correspondence Analysis and Weighted Metabolic Profiles Analysis

1 Introduction

2 Geometrical and Numerical Bases of Simplex Space

3 CA: Principle and Method

4 Weighted Metabolic Profiles Analysis

5 Application Example Combining CA and WMPA

References

Chapter Eleven. Strategies for Data Handling and Statistical Analysis in Metabolomics Studies

1 Introduction

2 General Characteristics of the Data

3 NMR Data Recording and Preprocessing: The Necessary Steps Prior to Statistical Analyses

4 LC/MS Data Recording and Preprocessing: The Necessary Steps Prior to Statistical Analyses

5 GC/MS Data Recording and Preprocessing: The Necessary Steps Prior to Statistical Analyses

6 Data Pretreatment

7 Basic Methods for Statistical Analysis: Possible Approaches

8 Reproducibility and Experimental Issues

9 Supervised Methods for Classification Problems: Potential for Statistical Bias

References

Chapter Twelve. Qualitative Modelling of Metabolic Networks

1 Introduction

2 Reconstruction, Storage and Sharing

3 Graph Formalism for Network Mining

4 Visualization of Metabolic Networks

5 Conclusion

References

Chapter Thirteen. Modelling Metabolic Networks—The Theories of Metabolism

1 Which Rate Equations for the Reactions of a Metabolic Network?

2 The Structure of Metabolic Network: The Stoichiometry Matrix

3 The Steady State

4 The Structure of Metabolic Network: The Elementary Flux Modes (efms)

5 Metabolic Control Analysis

6 Softwares and Tools for Kinetic Modelling

7 Conclusion: Protocol for the Study of Metabolic Networks at Steady State

References

Author Index

Subject Index