Metabolomics in Practice - Successful Strategies to Generate and Analyze Metabolic Data

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.From the Contents:* Sampling and Sample Preparation in Microbial Metabolomics* Tandem Mass Spectrometry Hyphenated with HPLC and UHPLC for Targeted Metabolomics* GC-MS, LC-MS, CE-MS and Ultrahigh Resolution MS (FTICR-MS) in Metabolomics * NMR-based metabolomics analysis* Potential of Microfluidics and Single Cell Analysis in Metabolomics * Data Processing in Metabolomics* Validation and Measurement Uncertainty in Metabolomic Studies* Metabolomics and its Role in the Study of Mammalian Systems and in Plant Sciences* Metabolomics in Biotechnology and Nutritional Metabolomicsand more.

List of contents

PrefaceTHE SAMPLING AND SAMPLE PREPARATION PROBLEM IN MICROBIAL METABOLOMICSIntroductionMicroorganisms and Their PropertiesSampling MethodsQuenchingMetabolite ExtractionApplication of 13C-Labeled Internal StandardsConclusionsTANDEM MASS SPECTROMETRY HYPHENATED WITH HPLC AND UHPLC FOR TARGETED METABOLOMICSIntroductionLC-MS-Based Targeted MetabolomicsLiquid ChromatographyMass SpectrometrySample PreparationRelative and Absolute QuantificationApplicationsSynopsisUNCERTAINTY OF MEASUREMENT IN QUANTITATIVE METABOLOMICSIntroductionUncertainties of Quantitative MS ExperimentsConcluding RemarksGAS CHROMATOGRAPHY AND COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY HYPHENATED WITH MASS SPECTROMETRY FOR TARGETED AND NONTARGETED METABOLOMICSIntroduction and ScopeSample Preparation for GC-Based Metabolite ProfilingGC-MS and GC X GC-TOFMS Instrumentation for MetabolomicsData Analysis Strategies and SoftwareIllustrative Examples and Concluding RemarksLC-MS-BASED NONTARGETED METABOLOMICSIntroductionLC-MS-Based Untargeted MetabolomicsStudy DesignSample PreparationAnalytical StrategiesData AnalysisMetabolite IdentificationApplicationsSynopsisTHE POTENTIAL OF ULTRAHIGH RESOLUTION MS (FTICR-MS) IN METABOLOMICSIntroductionMetabolomics TechnologiesPrinciples of FTICR-MSProceeding in MetabolomicsApplication Example in Metabolomics Using FTICR-MS Exhaled Breath CondensateConclusion and RemarksNMR-BASED METABOLOMICS ANALYSISIntroductionPlatforms for MetabolomicsNMR for MetabolomicsApplications of NMR-Based MetabolomicsFuture Prospects and ConclusionsPOTENTIAL OF MICROFLUIDICS AND SINGLE CELL ANALYSIS IN METABOLOMICS (MICROMETABOLOMICS)IntroductionSample Processing for MetabolomicsMicrofluidic Separations for Metabolic AnalysisMicrofluidics for Cellular AnalysisA Look ForwardDATA PROCESSING IN METABOLOMICSIntroduction and ScopeCharacteristics of Metabolomics DataTypes of Biological Questions AskedValidationOverview of MethodsMETABOLIC FLUX ANALYSISIntroductionPrerequisites for Flux StudiesStoichiometric Flux AnalysisLabeling Studies Using IsotopesState-of-Art 13C Flux AnalysisApplication of Metabolic Flux AnalysisRecent Advances in the FieldConcluding RemarksMETABOLOMICS: APPLICATION IN PLANT SCIENCESIntroductionSample PreparationAnalytical MethodsMetabolite IdentificationStructural Elucidation of Novel Metabolites and Validation of ModelConclusion and PerspectivesMETABOLOMICS AND ITS ROLE IN THE STUDY OF MAMMALIAN SYSTEMSIntroduction - From Early BeginningsHypothesis Generation or Hypothesis-Testing StudiesUntargeted, Semi-Targeted, and Targeted Analytical ExperimentsStudy and Experimental DesignSamples TypesQuality Assurance and Quality ControlMetabolite Annotation and IdentificationApplicationsMETABOLOMICS IN BIOTECHNOLOGY (MICROBIAL METABOLOMICS)IntroductionAnalytical Methods Applied for Microbial MetabolomicsCustom-Made Separation for Microbial MetabolomicsMicrobial Metabolomics with Higher ThroughputApplication of Microbial MetabolomicsConclusionNUTRITIONAL METABOLOMICSIntroductionThe Metabolome of Human Plasma and Urine: General ConsiderationsThe Food Metabolome and Its Signature in Human SamplesThe Variability of the Human Metabolome in Health and Disease StatesThe Dynamic Nature of the MetabolomeThe Future of Nutritional Metabolomics and Research NeedsIndex

About the author

Michael Lämmerhofer is Professor of Pharmaceutical (Bio)Analysis at the University of Tuebingen, Germany. Having obtained his academic degrees from the University of Graz, he spent one year as a post-doctoral fellow at the Department of Chemistry of the University of California, Berkeley (USA). Later he was Associate Professor at the Department of Analytical Chemistry of the University of Vienna (Austria). His current research is directed towards the targeted quantitative analysis of extracellular and intracellular metabolites, mainly with focus on applications in industrial biotechnology.

Wolfram Weckwerth is Professor and Head of the Department of Molecular Systems Biology at the University of Vienna, Austria. Having obtained his academic degrees from the Technical University of Berlin, Germany, he moved to the Max-Planck-Institute of Molecular Plant Physiology in Potsdam, Germany, where he pioneered metabolomic methods and integrated proteomic and computer-based approaches into a systems biology framework. In 2007 he took over a position as the head of a research lab in the German FORSYS systems biology initiative. In 2008 he was appointed as a professor and founded the Department of Molecular Systems Biology at the University of Vienna.

Summary

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.

From the Contents:

* Sampling and Sample Preparation in Microbial Metabolomics
* Tandem Mass Spectrometry Hyphenated with HPLC and UHPLC for Targeted Metabolomics
* GC-MS, LC-MS, CE-MS and Ultrahigh Resolution MS (FTICR-MS) in Metabolomics
* NMR-based metabolomics analysis
* Potential of Microfluidics and Single Cell Analysis in Metabolomics
* Data Processing in Metabolomics
* Validation and Measurement Uncertainty in Metabolomic Studies
* Metabolomics and its Role in the Study of Mammalian Systems and in Plant Sciences
* Metabolomics in Biotechnology and Nutritional Metabolomics

and more.

Product details

• Authors: Michael Lämmerhofer, Wolfram Weckwerth
• Assisted by: Michae Lämmerhofer (Editor), Michael Lämmerhofer (Editor), Michae Lämmerhofer (Prof. Dr.) (Editor), Michael Lämmerhofer (Prof. Dr.) (Editor), Weckwerth (Editor), Wolfram Weckwerth (Editor), Weckwerth (Prof. (Editor)
• Publisher: Wiley-VCH
• Languages: English
• Product format: Hardback
• Released: 01.01.2013
• EAN: 9783527330898
• ISBN: 978-3-527-33089-8
• No. of pages: 416
• Dimensions: 172 mm x 247 mm x 27 mm
• Weight: 1092 g
• Illustrations: 89 SW-Abb., 11 Farbabb., 17 Tabellen
• Subjects: Natural sciences, medicine, IT, technology > Chemistry > Organic chemistry; Chemie, Biochemie, Analytische Chemie, Life Sciences, genom, Biowissenschaften, Chemische Biologie, biotechnology, chemistry, Metabolomics, Analytical Chemistry, Biochemie u. Chemische Biologie, Biochemistry (Chemical Biology), Biotechnologie i. d. Chemie, Genomforschung u. Proteomik, Genomics & Proteomics