Section I. Analytical Technology
I.1. Gas Chromatography Mass Spectrometry .................... 3
J. Корка
1. Introduction ............................................ 3
2. GC-MS Profiling Technology in a Nutshell ................ 5
3. Short Excursion into Nomenclature and Definitions ...... 10
4. Present Challenges of GC-MS Profiling .................. 13
References ............................................. 17
I.2. Current Status and Forward Looking Thoughts on
LC/MS Metabolomics ..................................... 21
L.W. Sumner
1. Introduction ........................................... 21
2. Chromatography Theory .................................. 24
3. Limitations of Current Metabolic Profiling Approaches
and Proposed Solutions to Advance Metabolomics ......... 25
4. Future Directions and Forward-Looking Thoughts ......... 28
References ............................................. 30
I.3. Plant Metabolomics Strategies Based upon Quadrupole
Time of Flight Mass Spectrometry (QTOF-MS) ............. 33
H.A. Verhoeven, C.H. Ric de Vos, R.J. Bino,
and R.D. Hall
1. Introduction ........................................... 33
2. The Technology ......................................... 34
3. Data Analysis .......................................... 37
4. Application of QTOF MS-based Plant Metabolomics
Analyses ............................................... 38
5. Conclusions and Future Prospects ....................... 46
References ............................................. 46
I.4. Capillary HPLC ......................................... 49
Т. Ikegami, E. Fukusaki, and N. Tanaka
1. Introduction ........................................... 49
2. Monolithic Silica Columns for Micro HPLC ............... 49
3. Applications of Monolithic Silica Columns to
Metabolomics ........................................... 54
4. Two-Dimensional HPLC ................................... 55
5. Combination of Reversed-Phase HPLC and Other
Separation Modes ....................................... 59
6. Outlook ................................................ 61
References ............................................. 61
I.5. Capillary HPLC Coupled to Electrospray Ionization
Quadrupole Time-of-flight Mass Spectrometry ............ 65
S. Clemens, С. Böttcher, M. Franz, E. Willscher,
E. v.Roepenack-Lahaye, and D. Scheel
1. Introduction ........................................... 65
2. Extraction, Chromatography and Mass Spectrometry ....... 67
3. Potential and Limitations .............................. 72
4. Conclusions and Outlook ................................ 77
References ............................................. 78
I.6. NMR Spectroscopy in Plant Metabolomics ................. 81
J.L. Ward and M.H. Beale
1. Introduction ........................................... 81
2. High-throughput Screening by ID 1H-NMR ................. 82
3. Data Analysis .......................................... 84
4. Two-dimensional NMR .................................... 85
5. Stable Isotope Labelling ............................... 86
6. Hyphenated NMR ......................................... 87
7. Discussion: Applying NMR to Plant Metabolomics ......... 88
References ............................................. 89
I.7. Hetero-nuclear NMR-based Metabolomics .................. 93
J. Kikuchi and T. Hirayama
1. Introduction ........................................... 93
2. Historical Aspects of NMR Studies of Plant
Metabolism ............................................. 93
3. 1H-NMR-based Metabolomics .............................. 94
4. Use of Stable Isotope Labeling Technique to Enable
Monitoring of the Dynamic Movement of Metabolites ...... 94
5. Approach for Hetero-nuclear NMR-based Metabolomics ..... 95
6. Prospects for the Future ............................... 98
References ............................................. 99
Section II. Bioinformatics
II.1. Bioinformatics Approaches to Integrate Metabolomics
and Other Systems Biology Data ........................ 105
B. Mehrotra and R. Mendes
1. Introduction .......................................... 105
2. Databases ............................................. 107
3. Data Visualization .................................... 110
4. Data Analysis ......................................... 111
5. Conclusion ............................................ 112
References ............................................ 113
II.2. Chemometrics in Metabolomics - An Introduction ....... 117
J. Trygg, J. Gullberg, A.I. Johansson, P. Jonsson
and T. Moritz
1. Introduction .......................................... 117
2. Theory and Methods .................................... 118
3. Example: Metabolomics Study on Arabidopsis Mutants .... 125
4. Summary and Future Prospectives ....................... 126
References ............................................ 127
II.3. MapEditor for the Atomic Reconstruction of
Metabolism (ARM) ...................................... 129
M. Arita, Y. Fujiwara, and Y. Nakanishi
1. Introduction .......................................... 129
2. Definition of Metabolic Information ................... 131
3. Metabolic Map Editor .................................. 133
4. Applications .......................................... 137
5. Conclusions ........................................... 139
References ............................................ 139
II.4. AraCyc: Overview of an Arabidopsis Metabolism
Database and its Applications for Plant Research ...... 141
S.Y. Rhee, P. Zhang, H. Foerster, and C. Tissier
1. Introduction .......................................... 141
2. Database Content ...................................... 142
3. Search, Browse, and Analyze Functionalities ........... 145
4. Applications of AraCyc ................................ 149
5. Current Issues and Future Directions .................. 152
6. Conclusions ........................................... 152
References ............................................ 153
II.5. KaPPA-View: A Tool for Integrating Transcriptomic
and Metabolomic Data on Plant Metabolic Pathway
Maps .................................................. 155
T. Tokimatsu, N. Sakurai, H. Suzuki, and
D. Shibata
1. Introduction .......................................... 155
2. General Features of the KaPPA-View Tool ............... 155
3. Plant Metabolic Pathway Maps .......................... 158
4. Integration of Transcriptomic and Metabolomic Data
on Pathway Maps ....................................... 159
5. Comparison with Other Databases and Tools ............. 159
6. Limitations and Future Improvements ................... 160
7. Conclusions ........................................... 162
References ............................................ 163
II.6. KNApSAcK: A Comprehensive Species-Metabolite
Relationship Database ................................. 165
Y. Shinbo, Y. Nakamura, M. Altaf-Ul-Amin,
H. Asahi, K. Kurokawa, M. Arita, K. Saito,
D. Ohta, D. Shibata, and S. Kanaya
1. Introduction .......................................... 165
2. Search Options of the KNApSAcK Database ............... 166
3. Statistics of the Database ............................ 172
4. Classification Based on Common Metabolites ............ 177
5. Conclusion and Remarks ................................ 179
6. Access to KNApSAcK .................................... 179
References ............................................ 180
Section III. Applications
III.1. Systems Biology: A Renaissance of the Top-down
Approach for Plant Analysis ........................... 185
F. Carrari, N. Schauer, L. Willmitzer, and
A.R. Fernie
1. Introduction .......................................... 185
2. Re-emergence of Top-down Thinking ..................... 186
3. Systems Biology in Non-plant Systems .................. 186
4. Systems Biology in Plant Systems ...................... 188
5. Dynamic Profiling in Plant Cells ...................... 192
6. Conclusions and Future Perspectives ................... 195
References ............................................ 195
III.2. Systems-based Analysis of Plant Metabolism by
Integration of Metabolomics with Transcriptomics ...... 199
M.Y. Hirai, T. Tohge, and K. Saito
1. Introduction .......................................... 199
2. Understanding Whole Plant Metabolism - Our Aims and
Strategy .............................................. 199
3. Metabolome and Transcriptome Analyses ................. 200
4. Studies on Sulfur Metabolism .......................... 201
5. Studies on Anthocyanin Metabolism ..................... 206
6. Conclusions ........................................... 208
References ............................................ 209
III.3. Targeted Profiling of Fatty Acids and Related
Metabolites ........................................... 211
T.R. Larson and I.A. Graham
1. Introduction .......................................... 211
2. Metabolite Profiling Techniques Used to Study Plant
Lipid Metabolism ...................................... 213
3. Future Developments ................................... 223
References ............................................ 224
III.4. Metabolic Profiling and Quantification of
Carotenoids and Related Isoprenoids in Crop Plants .... 229
P.D. Fraser and P.M. Bramley
1. Introduction .......................................... 229
2. Analytical Methodologies Employed in the Analysis
of Carotenoids ........................................ 233
3. Examples of Carotenoid/isoprenoid Profiling ........... 237
4. Conclusions ........................................... 240
References ............................................ 240
III.5. Metabolomics and Gene Identification in Plant
Natural Product Pathways .............................. 243
R.A. Dixon, L. Achnine, B.E. Deavours, and
M. Naoumkina
1. Introduction .......................................... 243
2. Gene Discovery - Past and Present Strategies .......... 243
3. Enzyme Promiscuity in Natural Product Pathways ........ 246
4. Examples of the Use of Metabolomics in the
Elucidation of Gene Function .......................... 247
5. Single Cell or Isolated Tissue Metabolomics ........... 253
6. Concluding Remarks .................................... 256
References ............................................ 256
III.6. Metabolomic Analysis of Catharanthus roseus Using
NMR and Principal Component Analysis .................. 261
H.K. Kim, Y.H. Choi, and R. Verpoorte
1. Introduction .......................................... 261
2. Experimental Consideration for Metabolomics
Using NMR ............................................. 262
3. Application of NMR for Plant Metabolome ............... 266
4. Principal Component Analysis .......................... 273
5. Concluding Remarks .................................... 275
References ............................................ 275
III.7. Metabolomics of Plant Secondary Compounds: Profiling
of Catharanthus Cell Cultures ......................... 277
M. Oresic, H. Rischer, and K.-M. Oksman-Caldentey
1. Introduction .......................................... 277
2. Metabolomics as a Platform to Study Plant Secondary
Metabolites ........................................... 278
3. Case Study: Metabolic Profiling of Catharanthus
roseus Cells .......................................... 280
4. Protocol .............................................. 285
5. Perspectives .......................................... 286
References ............................................ 287
III.8. The Taxus Metabolome and the Elucidation of the
Taxol® Biosynthetic Pathway in Cell Suspension
Cultures .............................................. 291
R.E.B. Ketchum and R.B. Croteau
1. Introduction .......................................... 291
2. Results and Discussion ................................ 294
3. Protocol .............................................. 306
4. Conclusion ............................................ 307
References ............................................ 308
III.9. The Use of Non-targeted Metabolomics in
Plant Science ......................................... 311
T. Daskalchuk, P. Ahiahonu, D. Heath, and
Y. Yamazaki
1. Introduction .......................................... 311
2. Fundamental Investigations into Plant Metabolomics .... 313
3. Conclusion ............................................ 324
References ............................................ 324
III.10. Plant Metabolite Profiling for Industrial
Applications .......................................... 327
R.N. Trethewey
1. Introduction .......................................... 327
2. The Metabolome ........................................ 327
3. Profiling Technologies ................................ 328
4. High Throughput Metabolite Profiling .................. 332
5. Industrial Applications ............................... 335
6. Outlook ............................................... 338
References ............................................ 338
Subject Index ................................................. 341
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