Metabolomics: Methods and Protocols

About this book

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.

Contents

PART I. Metabolome analysis using gaschromatography coupled to mass spectrometry (GC/MS)1 Metabolite profiling in blood plasmaOliver Fiehn and Tobias Kind2 Non-Supervised Construction and Application of Mass Spectral and Retention Time Index Libraries from Time-of-Flight GC-MS Metabolite ProfilesAlexander Erban, Nicolas Schauer, Alisdair R. Fernie, Joachim Kopka3 Metabolomic profiling of natural volatiles: head space trapping - GC/MSYury M. Tikunov, Francel W.A. Verstappen & Robert D Hall PART II. Metabolomics - Data integration and data mining4 Integrative profiling of metabolites and proteins: improving pattern recognition and biomarker selection for systems level approachesKatja Morgenthal, Stefanie Wienkoop, Florian Wolschin, and Wolfram Weckwerth5 Integrating profiling data: using linear correlation to reveal co-regulation of transcript and metabolitesEwa Urbanczyk-Wochniak, Lothar Willmitzer and Alisdair Fernie 6 Visualization and Analysis of Molecular DataMatthias Scholz and Joachim Selbig7 A gentle guide to the analysis of metabolomic dataRalf Steuer, Katja Morgenthal, Wolfram Weckwerth, and Joachim Selbig PART III. Capillary electrophoresis coupled to mass spectrometry (CE/MS)8 CE-MS for MetabolomicsTomoyoshi SogaPART IV. Liquid chromatography coupled to mass spectrometry (LC/MS) for metabolomics and structural elucidation9 Application of LC-MS analysis in Metabolomics: Reversed-Phase Monolithic Capillary Chromatography and Hydrophilic Chromatography coupled to Electrospray Ionization Mass SpectrometryVladimir V. Tolstikov, Oliver Fiehn, and Nobuo TanakaPART V. Electrochemical detection of metabolites10 HPLC-Separations Coupled with Coulometric-Electrode Array Detectors A Unique Approach to MetabolomicsBruce S. Kristal, Yevgeniya I. Shurubor, Rima Kaddurah-Daouk, and Wayne R. MatsonPART VI. Metabolic Fluxes11 Determination of metabolic flux ratios from 13C-experiments and GC MS data: protocol and principlesAnnik Nanchen, Tobias Fuhrer and Uwe Sauer12 Understanding the Roadmap of Metabolism by Pathway AnalysisStefan Schuster, Axel von Kamp and Mikhail PachkovPART VII. NMR metabolome analysis13 Revealing the metabolome of animal tissues using 1H NMR spectroscopyMark R. Viant14 NMR Metabonomics - Methods for Drug Discovery and DevelopmentKarl-Heinz Ott and Nelly Aranibar

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