Metabolomics in Practice

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Opis: Metabolomics in Practice

Unlike other handbooks in this emerging field, this guide focuses on the challenges and critical parameters in running a metabolomics study, including such often-neglected issues as sample preparation, choice of separation and detection method, recording and evaluating data as well as method validation. By systematically covering the entire workflow, from sample preparation to data processing, the insight and advice offered here helps to clear the hurdles in setting up and running a successful analysis, resulting in high-quality data from every experiment. Based on more than a decade of practical experience in developing, optimizing and validating metabolomics approaches as a routine technology in the academic and industrial research laboratory, the lessons taught here are highly relevant for all systems-level approaches, whether in systems biology, biotechnology, toxicology or pharmaceutical sciences.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


Szczegóły: Metabolomics in Practice

Tytuł: Metabolomics in Practice
Producent: VCH
ISBN: 9783527330898
Rok produkcji: 2013
Ilość stron: 442
Oprawa: Twarda
Waga: 1.07 kg


Recenzje: Metabolomics in Practice

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Metabolomics in Practice

  • Producent: VCH
  • Oprawa: Twarda

Unlike other handbooks in this emerging field, this guide focuses on the challenges and critical parameters in running a metabolomics study, including such often-neglected issues as sample preparation, choice of separation and detection method, recording and evaluating data as well as method validation. By systematically covering the entire workflow, from sample preparation to data processing, the insight and advice offered here helps to clear the hurdles in setting up and running a successful analysis, resulting in high-quality data from every experiment. Based on more than a decade of practical experience in developing, optimizing and validating metabolomics approaches as a routine technology in the academic and industrial research laboratory, the lessons taught here are highly relevant for all systems-level approaches, whether in systems biology, biotechnology, toxicology or pharmaceutical sciences.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

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