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 Metabolomics

and more.

Preface

THE SAMPLING AND SAMPLE PREPARATION PROBLEM IN MICROBIAL METABOLOMICS
Introduction
Microorganisms and Their Properties
Sampling Methods
Quenching
Metabolite Extraction
Application of 13C-Labeled Internal Standards
Conclusions

TANDEM MASS SPECTROMETRY HYPHENATED WITH HPLC AND UHPLC FOR TARGETED METABOLOMICS
Introduction
LC-MS-Based Targeted Metabolomics
Liquid Chromatography
Mass Spectrometry
Sample Preparation
Relative and Absolute Quantification
Applications
Synopsis

UNCERTAINTY OF MEASUREMENT IN QUANTITATIVE METABOLOMICS
Introduction
Uncertainties of Quantitative MS Experiments
Concluding Remarks

GAS CHROMATOGRAPHY AND COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY HYPHENATED WITH MASS SPECTROMETRY FOR TARGETED AND NONTARGETED METABOLOMICS
Introduction and Scope
Sample Preparation for GC-Based Metabolite Profiling
GC-MS and GC X GC-TOFMS Instrumentation for Metabolomics
Data Analysis Strategies and Software
Illustrative Examples and Concluding Remarks

LC-MS-BASED NONTARGETED METABOLOMICS
Introduction
LC-MS-Based Untargeted Metabolomics
Study Design
Sample Preparation
Analytical Strategies
Data Analysis
Metabolite Identification
Applications
Synopsis

THE POTENTIAL OF ULTRAHIGH RESOLUTION MS (FTICR-MS) IN METABOLOMICS
Introduction
Metabolomics Technologies
Principles of FTICR-MS
Proceeding in Metabolomics
Application Example in Metabolomics Using FTICR-MS Exhaled Breath Condensate
Conclusion and Remarks

NMR-BASED METABOLOMICS ANALYSIS
Introduction
Platforms for Metabolomics
NMR for Metabolomics
Applications of NMR-Based Metabolomics
Future Prospects and Conclusions

POTENTIAL OF MICROFLUIDICS AND SINGLE CELL ANALYSIS IN METABOLOMICS (MICROMETABOLOMICS)
Introduction
Sample Processing for Metabolomics
Microfluidic Separations for Metabolic Analysis
Microfluidics for Cellular Analysis
A Look Forward

DATA PROCESSING IN METABOLOMICS
Introduction and Scope
Characteristics of Metabolomics Data
Types of Biological Questions Asked
Validation
Overview of Methods

METABOLIC FLUX ANALYSIS
Introduction
Prerequisites for Flux Studies
Stoichiometric Flux Analysis
Labeling Studies Using Isotopes
State-of-Art 13C Flux Analysis
Application of Metabolic Flux Analysis
Recent Advances in the Field
Concluding Remarks

METABOLOMICS: APPLICATION IN PLANT SCIENCES
Introduction
Sample Preparation
Analytical Methods
Metabolite Identification
Structural Elucidation of Novel Metabolites and Validation of Model
Conclusion and Perspectives

METABOLOMICS AND ITS ROLE IN THE STUDY OF MAMMALIAN SYSTEMS
Introduction -
From Early Beginnings
Hypothesis Generation or Hypothesis-Testing Studies
Untargeted, Semi-Targeted, and Targeted Analytical Experiments
Study and Experimental Design
Samples Types
Quality Assurance and Quality Control
Metabolite Annotation and Identification
Applications

METABOLOMICS IN BIOTECHNOLOGY (MICROBIAL METABOLOMICS)
Introduction
Analytical Methods Applied for Microbial Metabolomics
Custom-Made Separation for Microbial Metabolomics
Microbial Metabolomics with Higher Throughput
Application of Microbial Metabolomics
Conclusion

NUTRITIONAL METABOLOMICS
Introduction
The Metabolome of Human Plasma and Urine: General Considerations
The Food Metabolome and Its Signature in Human Samples
The Variability of the Human Metabolome in Health and Disease States
The Dynamic Nature of the Metabolome
The Future of Nutritional Metabolomics and Research Needs

Index

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.