Abstract:
Metabolomics: Methods and Protocols examines the state-of-the-art in metabolomic analysis. Leading researchers in the field present protocols for the application of complementary analytical methods, such as gas chromatography-mass spectrometry (GC-MS). Metabolomics: Methods and Protocols contains forward-looking protocols, which provide the essential groundwork for future efforts in elucidating the structure of the unknowns detected in metabolomic studies. Part I of this volume focuses on GC-MS techniques; specifically, attention is given to metabolite profiling in blood plasma, construction and application of mass spectral and retention time index libraries, and metabolomic profiling of natural volatiles. In Part II, emphasis shifts to data integration and data mining techniques, and specific protocols discuss improving pattern recognition and biomarker selection for systems level approaches, and visualization and analysis of molecular and metabolomic data. Parts III, IV, and V examine the coupling of capillary electrophoresis and mass spectrometry, classical reversed phase liquid chromatography-mass spectrometry, and electrochemical detection of metabolites using HPLC separations coupled with coulometric electrode array detectors. In Part VI, protocols for the determination of metabolic flux rates are presented and a theoretical framework for metabolic pathway network analysis is provided. The volume concludes with an examination of cutting-edge NMR protocols.
1. Metabolite Profiling in Blood Plasma
Oliver Fiehn; Tobias Kind
pp. 3-18
2. Nonsupervised Construction and Application of Mass Spectral and Retention Time Index Libraries From Time-of-Flight Gas ChromatographyMass Spectrometry Metabolite Profiles
Alexander Erban; Nicolas Schauer; Alisdair R. Fernie; Joachim Kopka
pp. 19-38
3. Metabolomic Profiling of Natural Volatiles: Headspace Trapping: GCMS
Yury M. Tikunov; Francel W. A. Verstappen; Robert D. Hall
pp. 39-54
4. Integrative Profiling of Metabolites and Proteins: Improving Pattern Recognition and Biomarker Selection for Systems Level Approaches
Katja Morgenthal; Stefanie Wienkoop; Florian Wolschin; Wolfram Weckwerth
pp. 57-76
5. Integrating Profiling Data: Using Linear Correlation to Reveal Coregulation of Transcript and Metabolites
Ewa Urbanczyk-Wochniak; Lothar Willmitzer; Alisdair R. Fernie
pp. 77-86
6. Visualization and Analysis of Molecular Data
Matthias Scholz; Joachim Selbig
pp. 87-104
7. A Gentle Guide to the Analysis of Metabolomic Data
Ralf Steuer; Katja Morgenthal; Wolfram Weckwerth; Joachim Selbig
pp. 105-126
8. Capillary ElectrophoresisMass Spectrometry for Metabolomics
Tomoyoshi Soga
pp. 129-138
9. Application of Liquid ChromatographyMass Spectrometry Analysis in Metabolomics: Reversed-Phase Monolithic Capillary Chromatography and Hydrophilic Chromatography Coupled to Electrospray IonizationMass Spectrometry
Vladimir V. Tolstikov; Oliver Fiehn; Nobuo Tanaka
pp. 141-156
10. High-Performance Liquid Chromatography Separations Coupled With Coulometric Electrode Array Detectors: A Unique Approach to Metabolomics
Bruce S. Kristal; Yevgeniya I. Shurubor; Rima Kaddurah-Daouk; Wayne R. Matson
pp. 159-174
11. Determination of Metabolic Flux Ratios From 13C-Experiments and Gas ChromatograpyhMass Spectrometry Data: Protocol and Principles
Annik Nanchen; Tobias Fuhrer; Uwe Sauer
pp. 177-198
12. Understanding the Roadmap of Metabolism by Pathway Analysis
Stefan Schuster; Axel von Kamp; Mikhail Pachkov
pp. 199-226
13. Revealing the Metabolome of Animal Tissues Using 1H Nuclear Magnetic Resonance Spectroscopy
Mark R. Viant
pp. 229-246
14. Nuclear Magnetic Resonance Metabonomics: Methods for Drug Discovery and Development
Karl-Heinz Ott; Nelly Aranibar
pp. 247-272
15. Practical Aspects of Uniform Stable Isotope Labeling of Higher Plants for Heteronuclear NMR-Based Metabolomics
Jun Kikuchi; Takashi Hirayama
pp. 273-286