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.

Table of Contents:
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