Metabolomics Perspectives

Metabolomics Perspectives

From Theory to Practical Application

1st Edition - March 15, 2022

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  • Editor: Jacopo Troisi
  • eBook ISBN: 9780323850636
  • Paperback ISBN: 9780323850629

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Description

Metabolomics Perspectives: From Theory to Practical Application is an expertly written volume, which provides a thorough description of the current state-of-the-art in the metabolomics field. The philosophy behind the book is to guide the reader in a step-by-step exploration of metabolomics experiments, ranging from sample preparation to data extraction, analysis and interpretation, and to discuss the main current applications and future perspectives of this emerging science. Armed with critical insights, coupled with a clear writing, the book consists of three main sections. The first one introduces the pivotal theoretical fundamentals and provides a comprehensive overview of the "wet" laboratory workflow, including protocol instructions and a detailed description of experimental methods and analytical techniques. The second section covers a wide range of topics in the context of data analysis, including guidance in exploratory analysis, supervised and unsupervised machine learning approaches and validation and optimization methods. In addition to the several examples reported in the text, the book features an R package, specifically designed to perform all the described algorithms, which is hosted on a companion website (www.metabolomicsperspectives.com) together with several sets of available metabolomic data. Finally, an extensive dissertation describes the latest advances and the major fields of interest for metabolomics applications, highlighting their crucial potentials for future biomedical research. Thus, this book represents a must-read for both experienced researchers, interested in metabolomics, and newcomers to the field.

Key Features

  • Provides an in-depth description of the metabolomics experimental workflow and its applications in life science and biomedical research
  • Features chapter contributions from the greatest international experts in the field
  • Includes an R package and several sets of metabolomics data, hosted on a companion website

Readership

Life science researchers in biochemistry, molecular biology, or cell biology; systems biology researchers; medical and health informaticists; clinical chemists and pharmaceutical scientists; analytical chemists; clinicians, and students.

Table of Contents

  • Cover image
  • Title page
  • Table of Contents
  • Copyright
  • List of contributors
  • Foreword
  • Introduction
  • Section 1: Fundamentals
  • Chapter 1. System biology
  • Abstract
  • Introduction
  • Genomics
  • Epigenetics
  • Transcriptomics
  • Proteomics
  • Metabolomics
  • References
  • Chapter 2. Experimental design in metabolomics
  • Abstract
  • Introduction
  • Applications of metabolomic experiments
  • Untargeted and targeted approaches
  • Analytical methodologies
  • Nuclear magnetic resonance
  • Sample preparation
  • Identification and quantification of metabolites
  • Quality control
  • Conclusion
  • References
  • Further reading
  • Chapter 3. Separation techniques
  • Abstract
  • The role of the separation processes in metabolomics research
  • Sample preparation
  • Fundamentals of chromatography
  • Liquid chromatography
  • Gas chromatography
  • Multidimensional chromatography
  • Other separation techniques
  • References
  • Chapter 4. Mass spectrometry in metabolomics
  • Abstract
  • Mass spectrometry
  • Mass spectrum
  • Mass spectrometer
  • Tandem mass spectrometry
  • Untargeted metabolomics in complex samples
  • Analytical techniques in mass spectrometry -based metabolomics
  • Applications
  • References
  • Further reading
  • Chapter 5. Nuclear magnetic resonance in metabolomics
  • Abstract
  • Introduction
  • Nuclear magnetic resonance spectroscopy
  • High-resolution magic-angle spinning nuclear magnetic resonance spectroscopy
  • Pure shift nuclear magnetic resonance
  • Recent advances
  • Advantages of nuclear magnetic resonance spectroscopy
  • Challenges and limitations
  • Sample preparation
  • Summary and future perspectives
  • References
  • Chapter 6. Targeted metabolomics
  • Abstract
  • Targeted metabolomics
  • Inborn errors of metabolism
  • Application of targeted metabolomics to the newborn screening of inborn errors of metabolism
  • Examples of inborn error of metabolism diagnosed by the newborn screening
  • Propionic acidemia
  • Glutaric acidemia
  • Isovaleric acidemia
  • Phenylketonuria
  • Hereditary tyrosinemias
  • Maple syrup urine disease
  • Conclusion
  • References
  • Chapter 7. Approaches in untargeted metabolomics
  • Abstract
  • Introduction
  • Local and nonlocal metabolomics effects
  • Untargeted metabolomics application
  • Metabolomics profiling
  • Cardiovascular disease
  • Neurodegenerative disease
  • Limitations
  • Sources of metabolome variability
  • Key trends in untargeted metabolomics
  • Moving metabolomics from laboratories to clinics
  • Metabolomics pipeline standardization
  • Sample size
  • Independent cohort to validate the results
  • Cause/effects disambiguation
  • Conclusion
  • References
  • Section 2: Data analysis
  • Chapter 8. Techniques for converting metabolomic data for analysis
  • Abstract
  • Introduction
  • Data preprocessing
  • Normalization
  • Data pretreatment
  • Conclusion
  • References
  • Chapter 9. Data analysis in metabolomics: from information to knowledge
  • Abstract
  • Introduction
  • Exploratory analysis
  • Unsupervised machine learning analysis
  • Supervised machine learning
  • Classification model validation
  • Class imbalance
  • Ensemble machine learning
  • Features selection
  • Hyperparameters optimization
  • Appendix
  • References
  • Chapter 10. Relevant metabolites’ selection strategies
  • Abstract
  • Introduction
  • Low-level variable selection
  • Medium-level variable selection
  • High-level variable selection
  • Heuristic approach
  • Concluding remarks
  • References
  • Chapter 11. Pathway analysis
  • Abstract
  • Metabolites ontology
  • Metabolic pathway analysis
  • Enrichment
  • Metabolite set enrichment analysis
  • Kolmogorov–Smirnov test
  • Tools for metabolomic pathway analysis
  • Conclusions
  • References
  • Section 3: Application
  • Chapter 12. Cell culture metabolomics and lipidomics
  • Abstract
  • Introduction
  • Sample processing and experimentation for cell culture lipidomics and metabolomics
  • Analysis of metabolic processes including metabolic flux
  • Cell culture for isolation of small extracellular vesicles
  • Isolation of small extracellular vesicles using ultracentrifugation
  • Isolation of small extracellular vesicles using tangential flow filtration
  • Sample preparation and analysis with nuclear magnetic resonance spectroscopy
  • Cell culture metabolomics and lipidomics data analysis
  • Machine learning and hybrid models and artificial intelligence for cell design
  • References
  • Chapter 13. Single cell metabolomics
  • Abstract
  • Introduction
  • Single-cell metabolomics in microbial technology
  • Single-cell metabolomics in plant science and agriculture
  • Diversified animal applications
  • Single-cell metabolomics in developmental biology
  • Single-cell metabolomics in aging and senescence study
  • Single-cell metabolomics in stem cell biology
  • Single-cell metabolomics in functional genomics
  • Single-cell metabolomics in nutrition research
  • Single-cell metabolomics in environmental biology
  • Single-cell metabolomics in system biology
  • Single-cell metabolomics in immunology
  • Single-cell metabolomics in detection of metabolite dynamicity and pathway modulation
  • Single-cell metabolomics in clinical metabolism and disease perspective
  • Conclusion and future prospect
  • References
  • Chapter 14. Gut microbiota-derived metabolites in host physiology
  • Abstract
  • Introduction
  • Metabolomics methods in host-microbiome studies
  • Fermentable metabolites and short chain fatty acids
  • Secondary bile acids
  • Amino acids- and tryptophan-derived metabolites
  • Additional microbially derived metabolites
  • Perspectives and future directions
  • References
  • Further reading
  • Chapter 15. MALDI–mass spectrometry imaging: the metabolomic visualization
  • Abstract
  • Introduction
  • Basics of MALDI mass spectrometry imaging
  • Matrix choice and application
  • Tissue preparation for MALDI mass spectrometry imaging analysis
  • MALDI mass spectrometry imaging instrumentation
  • MALDI mass spectrometry imaging of endogenous metabolites
  • Metabolite annotation and quantitation in MALDI mass spectrometry imaging
  • Conclusion and future perspectives
  • References
  • Chapter 16. Metabolomics for oncology
  • Abstract
  • Introduction
  • Reprogramming of cancer cell metabolism
  • Lactate shuttle due to tumor hypoxia and Warburg effect
  • Metabolism of arginine and ornithine involved in linking tricarboxylic acid and urea cycles
  • Lipid synthesis pathway
  • Nucleotide biosynthesis pathway
  • Applications and examples of human cancer metabolomics
  • Urine metabolomics studies
  • Tissue metabolomics studies
  • Fecal metabolomics studies
  • Saliva metabolomics studies
  • Metabolomics studies on other biological matrices
  • Conclusion
  • References
  • Chapter 17. Metabolomics as a tool for precision medicine
  • Abstract
  • Systems approaches and systems medicine
  • Individual phenotyping using nuclear magnetic resonance
  • Applications
  • References
  • Chapter 18. Metabolomics in public health
  • Abstract
  • Introduction
  • Data integration
  • System biology and metabolomics in publich health
  • Longitudinal and life-long studies in metabolomics
  • Quantitative methods are necessary
  • Big data and metabolomics in public health
  • Policies, training, and resources
  • Final remarks
  • References
  • Index

Product details

  • No. of pages: 684
  • Language: English
  • Copyright: © Academic Press 2022
  • Published: March 15, 2022
  • Imprint: Academic Press
  • eBook ISBN: 9780323850636
  • Paperback ISBN: 9780323850629

About the Editor

Jacopo Troisi

Author of more than 100 papers in international peer-reviewed journals, holder of several international patents, and speaker at dozen international conferences, Jacopo Troisi is an award-winning expert in the metabolomics field. After graduating Summa cum Laude in biotechnology, he joined Medical School in the prestigious “Scuola Medica Salernitana” at the University of Salerno (Italy). He also attended and completed studies in data analysis. Currently, he is a visiting professor of Metabolomics in both Salerno and Sannio Universities (Italy), cofounder and CEO at Theoreo srl, spin-off company of the University of Salerno, and COO at the European Biomedical Research Institute of Salerno (EBRIS). His research interests are mainly focused on metabolomic profiling to provide insights in human disease onset and for the development of diagnostic tools.

Affiliations and Expertise

Research Scientist and COO, European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy

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