Methodologies for Metabolomics: Experimental Strategies and Techniques

doi:10.1017/CBO9780511996634

Methodologies for Metabolomics

Experimental Strategies and Techniques

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Metabolomics, the global characterisation of the small molecule complement involved in metabolism, has evolved into a powerful suite of approaches for understanding the global physiological and pathological processes occurring in biological organisms. The diversity of metabolites, the wide range of metabolic pathways and their divergent biological contexts require a range of methodological strategies and techniques. Methodologies for Metabolomics provides a comprehensive description of the newest methodological approaches in metabolomic research. The most important technologies used to identify and quantify metabolites, including nuclear magnetic resonance and mass spectrometry, are highlighted. The integration of these techniques with classical biological methods is also addressed. Furthermore, the book presents statistical and chemometric methods for evaluation of the resultant data. The broad spectrum of topics includes a vast variety of organisms, samples and diseases, ranging from in vivo metabolomics in humans and animals to in vitro analysis of tissue samples, cultured cells and biofluids.

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Contents

Methodologies for Metabolomics - Half title page
pp i-ii
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Methodologies for Metabolomics - Title page
pp iii-iii
Experimental Strategies and Techniques
- By Norbert W. Lutz, Jonathan V. Sweedler, Ron A. Wevers
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Copyright page
pp iv-iv
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Contents
pp v-vii
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Contributors
pp viii-xii
- By J. William Allwood, Eleni T. Bairaktari, Jean-Pierre Bellocq, Malika A. Benahmed, Hanne Christine Bertram, Zaver M. Bhujwalla, Ulrich Braumann, Juan Casado-Vela, Marta Cascante, Arancha Cebrián, Albert Chen, Man Ho Choi, Bong Chul Chung, Yuen-Li Chung, Morten Rahr Clausen, Patrick J. Cozzone, Ralph J. DeBerardinis, Julien Detour, Santiago Díaz-Moralli, Warwick B. Dunn, Karim Elbayed, Udo Engelke, Teresa W.-M. Fan, Ana M. Gil, Kristine Glunde, Markus Godejohann, Teresa Gómez del Pulgar, Royston Goodacre, Angelina Goudswaard, Gonçalo Graça, Richard W. Gross, Herbert H. Hill, Ralph E. Hurd, Alessio Imperiale, Kimberly A. Kaplan, Neil L. Kelleher, Michael A. Kiebish, Ann M. Knolhoff, Christina E. Kostara, Juan Carlos Lacal, Andrew N. Lane, Martin O. Leach, Norbert W. Lutz, Elizabeth Maher, Craig R. Malloy, Isaac Marin-Valencia, Laura Menchén, Bruce Mickey, Fanny Mochel, Éva Morava, François-Marie Moussallieh, Izzie J. Namer, Peter Nemes, Ioanna Ntai, Geoffrey S. Payne, Marie-France Penet, Martial Piotto, Stanislav S. Rubakhin, Elsa Sánchez-López, A. Dean Sherry, Bindesh Shrestha, Jonathan V. Sweedler, Akos Vertes, Mark R. Viant, Ralf J. M. Weber, Ron Wehrens, Ron A. Wevers, Catherine L. Winder, David S. Wishart, Kui Yang, Yi-Fen Yen
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Section 1 - Basic Methodological Strategies in Metabolomic Research
pp 1-76
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1 - Exploring the Human Metabolome by Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry
pp 3-29
- By David S. Wishart
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2 - Methodological Requirements for Lipidomics Research
pp 30-53
- By Kui Yang, Michael A. Kiebish, Richard W. Gross
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3 - Biological Methods for Metabolic Research
pp 54-76
- By Arancha Cebrián, Laura Menchén, Elsa Sánchez-López, Juan Casado-Vela, Santiago Díaz-Moralli, Marta Cascante, Teresa Gómez del Pulgar, Juan Carlos Lacal
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Section 2 - Metabolomic Mass Spectrometry: Experimental Techniques and Bioinformatics
pp 77-224
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4 - Considerations in Sample Preparation, Collection, and Extraction Approaches Applied in Microbial, Plant, and Mammalian Metabolic Profiling
pp 79-118
- By J. William Allwood, Catherine L. Winder, Warwick B. Dunn, Royston Goodacre
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5 - Mass Spectrometry–Based Methodologies for Single-Cell Metabolite Detection and Identification
pp 119-139
- By Ann M. Knolhoff, Peter Nemes, Stanislav S. Rubakhin, Jonathan V. Sweedler
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6 - Direct Metabolomics from Tissues and Cells: Laser Ablation Electrospray Ionization for Small Molecule and Lipid Characterization
pp 140-158
- By Akos Vertes, Bindesh Shrestha, Peter Nemes
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7 - Bioinformatic Approaches to Processing and Annotation of High-Resolution Mass Spectrometry Data
pp 159-173
- By Ralf J. M. Weber, Mark R. Viant
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8 - Approaches for Natural Product Detection and Structural Elucidation Using Mass Spectrometry with High Mass Accuracy
pp 174-184
- By Ioanna Ntai, Neil L. Kelleher
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9 - Metabolomics Using Ion Mobility Mass Spectrometry
pp 185-204
- By Kimberly A. Kaplan, Herbert H. Hill
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10 - Metabolomics via Biomedical Mass Spectrometry: From Sampling to Clinical Applications
pp 205-224
- By Bong Chul Chung, Man Ho Choi
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Section 3 - Metabolomics of Biofluids: Nuclear Magnetic Resonance Spectroscopy and Chemometrics
pp 225-332
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11 - Analytical Techniques in Metabolomics Integrating Nuclear Magnetic Resonance Spectroscopy and Chromatography with Mass Spectrometry
pp 227-243
- By Ulrich Braumann, Markus Godejohann
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12 - Chemometric Methods in Nuclear Magnetic Resonance–Based Body Fluid Analysis
pp 244-256
- By Ron Wehrens, Udo Engelke
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13 - Nuclear Magnetic Resonance of Cerebrospinal Fluid: The Neurometabolome
pp 257-270
- By Fanny Mochel
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14 - Nuclear Magnetic Resonance–Based Saliva Metabolomics
pp 271-280
- By Hanne Christine Bertram, Morten Rahr Clausen
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15 - Nuclear Magnetic Resonance Methods for Metabolomic Investigation of Amniotic Fluid
pp 281-298
- By Ana M. Gil, Gonçalo Graça
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16 - Nuclear Magnetic Resonance Analysis and Genetic Metabolic Disease
pp 299-316
- By Udo Engelke, Angelina Goudswaard, Éva Morava, Ron A. Wevers
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17 - Lipid Profiling in Health and Disease
pp 317-332
- By Christina E. Kostara, Eleni T. Bairaktari
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Section 4 - Metabolomic Nuclear Magnetic Resonance Spectroscopy Techniques for Body Tissue Analysis
pp 333-584
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18 - Magnetic Resonance Spectroscopy in Investigating the Cancer Metabolome in Preclinical Model Systems
pp 335-376
- By Marie-France Penet, Zaver M. Bhujwalla, Kristine Glunde
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19 - Phospholipidomics by Phosphorus Nuclear Magnetic Resonance Spectroscopy of Tissue Extracts
pp 377-414
- By Norbert W. Lutz, Patrick J. Cozzone
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20 - Carbon-13 Nuclear Magnetic Resonance for Analysis of Metabolic Pathways
pp 415-445
- By Craig R. Malloy, Elizabeth Maher, Isaac Marin-Valencia, Bruce Mickey, Ralph J. DeBerardinis, A. Dean Sherry
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21 - Hyperpolarized Nuclear Magnetic Resonance Spectroscopy: A New Method for Metabolomic Research
pp 446-471
- By Ralph E. Hurd, Yi-Fen Yen, Albert Chen
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Methodologies for Metabolomics

Experimental Strategies and Techniques

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Contents

Methodologies for Metabolomics - Half title page
pp i-ii

Methodologies for Metabolomics - Title page
pp iii-iii

Copyright page
pp iv-iv

Contents
pp v-vii

Contributors
pp viii-xii

Section 1 - Basic Methodological Strategies in Metabolomic Research
pp 1-76

1 - Exploring the Human Metabolome by Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry
pp 3-29

2 - Methodological Requirements for Lipidomics Research
pp 30-53

3 - Biological Methods for Metabolic Research
pp 54-76

Section 2 - Metabolomic Mass Spectrometry: Experimental Techniques and Bioinformatics
pp 77-224

4 - Considerations in Sample Preparation, Collection, and Extraction Approaches Applied in Microbial, Plant, and Mammalian Metabolic Profiling
pp 79-118

5 - Mass Spectrometry–Based Methodologies for Single-Cell Metabolite Detection and Identification
pp 119-139

6 - Direct Metabolomics from Tissues and Cells: Laser Ablation Electrospray Ionization for Small Molecule and Lipid Characterization
pp 140-158

7 - Bioinformatic Approaches to Processing and Annotation of High-Resolution Mass Spectrometry Data
pp 159-173

8 - Approaches for Natural Product Detection and Structural Elucidation Using Mass Spectrometry with High Mass Accuracy
pp 174-184

9 - Metabolomics Using Ion Mobility Mass Spectrometry
pp 185-204

10 - Metabolomics via Biomedical Mass Spectrometry: From Sampling to Clinical Applications
pp 205-224

Section 3 - Metabolomics of Biofluids: Nuclear Magnetic Resonance Spectroscopy and Chemometrics
pp 225-332

11 - Analytical Techniques in Metabolomics Integrating Nuclear Magnetic Resonance Spectroscopy and Chromatography with Mass Spectrometry
pp 227-243

12 - Chemometric Methods in Nuclear Magnetic Resonance–Based Body Fluid Analysis
pp 244-256

13 - Nuclear Magnetic Resonance of Cerebrospinal Fluid: The Neurometabolome
pp 257-270

14 - Nuclear Magnetic Resonance–Based Saliva Metabolomics
pp 271-280

15 - Nuclear Magnetic Resonance Methods for Metabolomic Investigation of Amniotic Fluid
pp 281-298

16 - Nuclear Magnetic Resonance Analysis and Genetic Metabolic Disease
pp 299-316

17 - Lipid Profiling in Health and Disease
pp 317-332

Section 4 - Metabolomic Nuclear Magnetic Resonance Spectroscopy Techniques for Body Tissue Analysis
pp 333-584

18 - Magnetic Resonance Spectroscopy in Investigating the Cancer Metabolome in Preclinical Model Systems
pp 335-376

19 - Phospholipidomics by Phosphorus Nuclear Magnetic Resonance Spectroscopy of Tissue Extracts
pp 377-414

20 - Carbon-13 Nuclear Magnetic Resonance for Analysis of Metabolic Pathways
pp 415-445

21 - Hyperpolarized Nuclear Magnetic Resonance Spectroscopy: A New Method for Metabolomic Research
pp 446-471

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Methodologies for Metabolomics

Experimental Strategies and Techniques

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