1;Preface;6 2;Contents;7 3;List of Contributors;13 4;Section I Analytical Technology;20 4.1;I.1 Gas ChromatographyMass Spectrometry;21 4.1.1;1 Introduction;21 4.1.2;2 GC-MS Pro.ling Technology in a Nutshell;23 4.1.3;3 Short Excursion into Nomenclature and De.nitions;28 4.1.4;4 Present Challenges of GC-MS Pro.ling;31 4.1.5;References;35 4.2;I.2 Current Status and Forward Looking Thoughts on LC/ MSMetabolomics;39 4.2.1;1 Introduction;39 4.2.2;2 Chromatography Theory;42 4.2.3;3 Limitations of CurrentMetabolic Pro.ling Approaches and Proposed Solutions to AdvanceMetabolomics;43 4.2.4;4 Future Directions and Forward-Looking Thoughts;46 4.2.5;References;48 4.3;I.3 PlantMetabolomics Strategies Based upon Quadrupole Time of FlightMass Spectrometry ( QTOF- MS);51 4.3.1;1 Introduction;51 4.3.2;2 TheTechnology;52 4.3.3;3 Data Analysis;55 4.3.4;4 Application of QTOF MS-based PlantMetabolomics Analyses;56 4.3.5;5 Conclusions and Future Prospects;64 4.3.6;References;64 4.4;I.4 Capillary HPLC;67 4.4.1;1 Introduction;67 4.4.2;2 Monolithic Silica Columns for Micro HPLC;67 4.4.3;3 Applications ofMonolithic Silica Columns toMetabolomics;72 4.4.4;4 Two-Dimensional HPLC;73 4.4.5;5 Combination of Reversed-Phase HPLC and Other SeparationModes;77 4.4.6;6 Outlook;79 4.4.7;References;79 4.5;I.5 Capillary HPLC Coupled to Electrospray Ionization Quadrupole Time- of- . ightMass Spectrometry;82 4.5.1;1 Introduction;82 4.5.2;2 Extraction, Chromatography andMass Spectrometry;84 4.5.3;3 Potential and Limitations;89 4.5.4;4 Conclusions and Outlook;94 4.5.5;References;95 4.6;I.6 NMR Spectroscopy in PlantMetabolomics;97 4.6.1;1 Introduction;97 4.6.2;2 High-throughput Screening by 1D H-NMR;98 4.6.3;3 Data Analysis;100 4.6.4;4 Two-dimensional NMR;101 4.6.5;5 Stable Isotope Labelling;102 4.6.6;6 HyphenatedNMR;103 4.6.7;7 Discussion: Applying NMR to PlantMetabolomics;104 4.6.8;References;105 4.7;I.7 Hetero-nuclear NMR-basedMetabolomics;108 4.7.1;1 Introduction;108 4.7.2;2 Historical Aspects of NMR Studies of PlantMetabolism;108 4.7.3;3 H-NMR-basedMetabolomics;109 4.7.4;4 Use of Stable Isotope Labeling Technique to Enable Monitoring of the DynamicMovement ofMetabolites;109 4.7.5;5 Approach for Hetero-nuclear NMR-basedMetabolomics;110 4.7.6;6 Prospects for the Future;113 4.7.7;References;114 5;Section II Bioinformatics;117 5.1;II.1 Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data;118 5.1.1;1 Introduction;118 5.1.2;2 Databases;120 5.1.3;3 Data Visualization;123 5.1.4;4 Data Analysis;124 5.1.5;5 Conclusion;125 5.1.6;References;126 5.2;II.2 Chemometrics inMetabolomics - An Introduction;129 5.2.1;1 Introduction;129 5.2.2;2 Theory andMethods;130 5.2.3;3 Example: Metabolomics Study on ArabidopsisMutants;137 5.2.4;4 Summary and Future Prospectives;138 5.2.5;References;139 5.3;II.3 Map Editor for the Atomic Reconstruction ofMetabolism ( ARM);141 5.3.1;1 Introduction;141 5.3.2;2 Definition ofMetabolic Information;143 5.3.3;3 MetabolicMap Editor;145 5.3.4;4 Applications;149 5.3.5;5 Conclusions;151 5.3.6;References;151 5.4;II.4 AraCyc: Overview of an ArabidopsisMetabolism Database and its Applications for Plant Research;152 5.4.1;1 Introduction;152 5.4.2;2 DatabaseContent;153 5.4.3;3 Search, Browse, and Analyze Functionalities;156 5.4.4;4 Applications of AraCyc;160 5.4.5;5 Current Issues and Future Directions;163 5.4.6;6 Conclusions;163 5.4.7;References;164 5.5;II.5 KaPPA-View: A Tool for Integrating Transcriptomic andMetabolomic Data on PlantMetabolic PathwayMaps;166 5.5.1;1 Introduction;166 5.5.2;2 General Features of the KaPPA-View Tool;166 5.5.3;3 PlantMetabolic PathwayMaps;169 5.5.4;4 Integration of Transcriptomic andMetabolomic Data on PathwayMaps;170 5.5.5;5 Comparison with Other Databases and Tools;170 5.5.6;6 Limitations and Future Improvements;171 5.5.7;7 Conclusions;173 5.5.8;References;174 5.6;II.6 KNApSAcK: A Comprehensive Species-Metabolite Relationship Database;175 5.6.1;1 Introduction;175 5.6.2;2 Search Options of the KNApSAcK Da