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Computational Methods and Data Analysis for Metabolomics

  • Book
  • © 2020

Overview

Editors:
  1. Shuzhao Li

    1. Department of Medicine, Emory University School of Medicine, Atlanta, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2104)

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xi
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  2. Overview of Experimental Methods and Study Design in Metabolomics, and Statistical and Pathway Considerations

    • Stephen Barnes
    Pages 1-10

  3. Metabolomics Data Processing Using XCMS

    • Xavier Domingo-Almenara, Gary Siuzdak
    Pages 11-24

  4. Metabolomics Data Preprocessing Using ADAP and MZmine 2

    • Xiuxia Du, Aleksandr Smirnov, Tomáš Pluskal, Wei Jia, Susan Sumner
    Pages 25-48

  5. Metabolomics Data Processing Using OpenMS

    • Marc Rurik, Oliver Alka, Fabian Aicheler, Oliver Kohlbacher
    Pages 49-60

  6. Analysis of NMR Metabolomics Data

    • Wimal Pathmasiri, Kristine Kay, Susan McRitchie, Susan Sumner
    Pages 61-97

  7. Key Concepts Surrounding Studies of Stable Isotope-Resolved Metabolomics

    • Stephen F. Previs, Daniel P. Downes
    Pages 99-120

  8. Extracting Biological Insight from Untargeted Lipidomics Data

    • Jennifer E. Kyle
    Pages 121-137

  9. Overview of Tandem Mass Spectral and Metabolite Databases for Metabolite Identification in Metabolomics

    • Zhangtao Yi, Zheng-Jiang Zhu
    Pages 139-148

  10. METLIN: A Tandem Mass Spectral Library of Standards

    • J. Rafael Montenegro-Burke, Carlos Guijas, Gary Siuzdak
    Pages 149-163

  11. Metabolomic Data Exploration and Analysis with the Human Metabolome Database

    • David S. Wishart
    Pages 165-184

  12. De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4

    • Marcus Ludwig, Markus Fleischauer, Kai Dührkop, Martin A. Hoffmann, Sebastian Böcker
    Pages 185-207

  13. Annotation of Specialized Metabolites from High-Throughput and High-Resolution Mass Spectrometry Metabolomics

    • Thomas Naake, Emmanuel Gaquerel, Alisdair R. Fernie
    Pages 209-225

  14. Feature-Based Molecular Networking for Metabolite Annotation

    • Vanessa V. Phelan
    Pages 227-243

  15. A Bioinformatics Primer to Data Science, with Examples for Metabolomics

    • W. Stephen Pittard, Cecilia “Keeko” Villaveces, Shuzhao Li
    Pages 245-263

  16. The Essential Toolbox of Data Science: Python, R, Git, and Docker

    • W. Stephen Pittard, Shuzhao Li
    Pages 265-311

  17. Predictive Modeling for Metabolomics Data

    • Tusharkanti Ghosh, Weiming Zhang, Debashis Ghosh, Katerina Kechris
    Pages 313-336

  18. Using MetaboAnalyst 4.0 for Metabolomics Data Analysis, Interpretation, and Integration with Other Omics Data

    • Jasmine Chong, Jianguo Xia
    Pages 337-360

  19. Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data

    • Jake P. N. Hattwell, Janna Hastings, Olivia Casanueva, Horst Joachim Schirra, Michael Witting
    Pages 361-386

  20. Pathway Analysis for Targeted and Untargeted Metabolomics

    • Alla Karnovsky, Shuzhao Li
    Pages 387-400
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Keywords

About this book

This book provides a comprehensive guide to scientists, engineers, and students that employ metabolomics in their work, with an emphasis on the understanding and interpretation of the data. Chapters guide readers through common tools for data processing, using database resources, major techniques in data analysis, and integration with other data types and specific scientific domains. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, practical guidance of methods and techniques, useful web supplements, and connect the steps from experimental metabolomics to scientific discoveries.

Authoritative and cutting-edge, Computational Methods and Data Analysis for Metabolomics to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Department of Medicine, Emory University School of Medicine, Atlanta, USA

    Shuzhao Li

Bibliographic Information

  • Book Title: Computational Methods and Data Analysis for Metabolomics

  • Editors: Shuzhao Li

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0239-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0238-6Published: 18 January 2020

  • Softcover ISBN: 978-1-0716-0241-6Published: 18 January 2021

  • eBook ISBN: 978-1-0716-0239-3Published: 17 January 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 491

  • Number of Illustrations: 56 b/w illustrations, 119 illustrations in colour

  • Topics: Metabolomics, Computational Biology/Bioinformatics

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