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Metabolomics in practice : successful strategies to generate and analyze metabolic data / edited by Michael Lammerhofer and Wolfram Weckwerth. -- Weinheim : Wiley-VCH, c2013. – (58.1761/M587m) |
Contents
CONTENTS
List of Contributors XV
Preface XXIII
1 The Sampling and Sample Preparation Problem in Microbial Metabolomics 1
Walter M. van Gulik， Andre B. Canelas， Reza M. Seifar， and Joseph J. Heijnen
1.1 Introduction 1
1.2 Microorganisms and Their Properties 1
1.3 Sampling Methods 2
1.4 Quenching 4
1.5 Metabolite Extraction 9
1.6 Application of 13C-Labeled Internal Standards 13
1.7 Conclusions 17
References 18
2 Tandem Mass Spectrometry Hyphenated with HPLC and UHPLC for Targeted Metabolomics 21
Gerard Hopfgartner and Emmanuel Varesio
2.1 Introduction 21
2.2 LC-MS-Based Targeted Metabolomics 22
2.3 Liquid Chromatography 22
2.4 Mass Spectrometry 27
2.5 Sample Preparation 30
2.6 Relative and Absolute Quantification 31
2.7 Applications 32
2.8 Synopsis 34
References 35
3 Uncertainty of Measurement in Quantitative Metabolomics 39
Raffaele Guerrasio， Christina Haberhauer-Troyer， Stefan Neubauer， Kristaps Klavins， Madeleine Werneth， Gunda Koellensperger， and Stephen Hann
3.1 Introduction 39
3.2 Uncertainties of Quantitative MS Experiments 48
3.3 Concluding Remarks 66
Abbreviations 66
Acknowledgment 67
References 67
4 Gas Chromatography and Comprehensive Two-Dimensional Gas Chromatography Hyphenated with Mass Spectrometry for Targeted and Nontargeted Metabolomics 69
Song Yang， Jamin C. Hoggard， Mary E. Lidstrom， and Robert E. Synovec
4.1 Introduction and Scope 69
4.2 Sample Preparation for GC-Based Metabolite Profiling 71
4.3 GC--MS and GC × GC--TOFMS Instrumentation for Metabolomics 74
4.4 Data Analysis Strategies and Software 82
4.5 Illustrative Examples and Concluding Remarks 88
References 89
5 LC-MS-Based Nontargeted Metabolomics 93
Georgios A. Theodoridis， Helen G. Gika， and Ian D. Wilson
5.1 Introduction 93
5.2 LC-MS-Based Untargeted Metabolomics 94
5.3 Study Design 98
5.4 Sample Preparation 100
5.5 Analytical Strategies 103
5.6 Data Analysis 104
5.7 Metabolite Identification 107
5.8 Applications 109
5.9 Synopsis 112
References 113
6 The Potential of Ultrahigh Resolution MS (FTICR-MS) in Metabolomics 117
Franco Moritz， Sara Forcisi， Mourad Harir， Basem Kanawati， Marianna Lucio， Dimitrios Tziotis， and Philippe Schmitt-Kopplin
6.1 Introduction 117
6.2 Metabolomics Technologies 118
6.3 Principles of FTICR-MS 121
6.4 Proceeding in Metabolomics 126
6.5 Application Example in Metabolomics Using FTICR-MS Exhaled Breath Condensate 128
6.6 Conclusion and Remarks 134
References 134
7 The Art and Practice of Lipidomics 137
Koen Sandra， Ruben t'Kindt， Lucie Jorge， and Pat Sandra Abbreviations 137
7.1 Introduction 139
7.2 Lipid Diversity 140
7.3 Tackling the Lipidome: State-of-the-Art 141
7.4 LC-MS-Based Lipidomics 146
7.5 GC-MS-Based Lipidomics 165
7.6 Conclusion 172
References 173
8 The Role of CE--MS in Metabolomics 177
Rawi Ramautar， Govert W. Somsen， and Gerhardus J. de Jong Abbreviations 177
8.1 Introduction 177
8.2 CE--MS 179
8.3 Sample Pretreatment 185
8.4 Data Analysis 187
8.5 Applications 190
8.6 Conclusions and Perspectives 203
References 206
9 NMR-Based Metabolomics Analysis 209
Andrea Lubbe， Kashif Ali， Robert Verpoorte， and Young Hae Choi
9.1 Introduction 209
9.2 Platforms for Metabolomics 210
9.3 NMR for Metabolomics 219
9.4 Applications of NMR-Based Metabolomics 228
9.5 Future Prospects and Conclusions 233
References 234
10 Potential of Microfluidics and Single Cell Analysis in Metabolomics (Micrometabolomics) 239
Meghan M. Mensack， Ryan E. Holcomb， and Charles S. Henry
10.1 Introduction 239
10.2 Sample Processing for Metabolomics 240
10.3 Microfluidic Separations for Metabolic Analysis 243
10.4 Microfluidics for Cellular Analysis 247
10.5 A Look Forward 254
References 256
11 Data Processing in Metabolomics 261
Age K. Smilde， Margriet M.W.B. Hendriks， Johan A. Westerhuis， and Huub C.J. Hoefsloot
11.1 Introduction and Scope 261
11.2 Characteristics of Metabolomics Data 261
11.3 Types of Biological Questions Asked 264
11.4 Validation 265
11.5 Overview of Methods 272
References 283
12 Metabolic Flux Analysis 285
Christoph Wittmann and Jean-Charles Portais
12.1 Introduction 285
12.2 Prerequisites for Flux Studies 287
12.3 Stoichiometric Flux Analysis 290
12.4 Labeling Studies Using Isotopes 292
12.5 State-of-Art 13C Flux Analysis 296
12.6 Application of Metabolic Flux Analysis 303
12.7 Recent Advances in the Field 307
12.8 Concluding Remarks 308
Acknowledgments 308
References 308
13 Metabolomics: Application in Plant Sciences 313
Gaetan Glauser， Julien Boccard， Jean-Luc Wolfender， and Serge Rudaz
13.1 Introduction 313
13.2 Sample Preparation 314
13.3 Analytical Methods 316
13.4 Metabolite Identification 330
13.5 Structural Elucidation of Novel Metabolites and Validation of Model 334
13.6 Conclusion and Perspectives 336
Acknowledgments 337
References 337
14 Metabolomics and Its Role in the Study of Mammalian Systems 345
Warwick B. Dunn， Mamas Mamas， and Alexander Heazell
14.1 Introduction -- From Early Beginnings 345
14.2 Hypothesis Generation or Hypothesis-Testing Studies 347
14.3 Untargeted， Semi-Targeted， and Targeted Analytical Experiments 348
14.4 Study and Experimental Design 350
14.5 Sample Types 355
14.6 Quality Assurance and Quality Control 360
14.7 Metabolite Annotation and Identification 365
14.8 Applications 369
Acknowledgments 373
References 373
15 Metabolomics in Biotechnology (Microbial Metabolomics) 379
Marco Oldiges， Stephan Noack， and Nicole Paczia
15.1 Introduction 379
15.2 Analytical Methods Applied for Microbial Metabolomics 382
15.3 Custom-Made Separation for Microbial Metabolomics 384
15.4 Microbial Metabolomics with Higher Throughput 385
15.5 Application of Microbial Metabolomics 386
15.6 Conclusion 388
References 388
16 Nutritional Metabolomics 393
Hannelore Daniel
16.1 Introduction 393
16.2 The Metabolome of Human Plasma and Urine: General Considerations 393
16.3 The Food Metabolome and Its Signature in Human Samples 396
16.4 The Variability of the Human Metabolome in Health and Disease States 398
16.5 The Dynamic Nature of the Metabolome 400
16.6 The Future of Nutritional Metabolomics and Research Needs 402
References 403
Index 407
