Metabolomics: Methods and Protocols

Weckwerth, Wolfram
Pages: 312
ISBN: 978-1588295613
Publisher:Humana Press


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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,
  • metabolomic profiling of natural volatiles.

In Part II, emphasis shifts to

  • data integration and data mining techniques
  • specific protocols discuss improving pattern recognition and biomarker selection for systems level approaches
  • 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
  • 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.

Table of contents:

  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 Chromatography–Mass Spectrometry Metabolite Profiles
    Alexander Erban, Nicolas Schauer, Alisdair Fernie, Joachim Kopka
    pp. 19-38
  3. Metabolomic Profiling of Natural Volatiles: Headspace Trapping: GC–MS
    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 Electrophoresis–Mass Spectrometry for Metabolomics
    Tomoyoshi Soga
    pp. 129-138
  9. Application of Liquid Chromatography–Mass Spectrometry Analysis in Metabolomics: Reversed-Phase Monolithic Capillary Chromatography and Hydrophilic Chromatography Coupled to Electrospray Ionization–Mass 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 Chromatograpyh–Mass 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