Computational methods and data analysis for metabolomics
Author(s)
Bibliographic Information
Computational methods and data analysis for metabolomics
（Methods in molecular biology / John M. Walker, series editor, v. 2104）（Springer protocols）
Humana Press, 2020
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
1. Overview of Experimental Methods and Study Design in Metabolomics, and Statistical and Pathway Considerations Stephen Barnes
2. Metabolomics Data Processing using XCMS
Xavier Domingo-Almenara and Gary Siuzdak
3. Metabolomics Data Preprocessing using ADAP and MZmine 2
Xiuxia Du, Aleksandr Smirnov, Tomas Pluskal, Wei Jia, and Susan Sumner
4. Metabolomics Data Processing using OpenMS
Marc Rurik, Oliver Alka, Fabian Aicheler, and Oliver Kohlbacher
5. Analysis of NMR Metabolomics Data
Wimal Pathmasiri, Kristine Kay, Susan McRitchie, and Susan Sumner
6. Key Concepts Surrounding Studies of Stable Isotope Resolved Metabolomics
Stephen F. Previs and Daniel P. Downes
7. Extracting Biological Insight from Untargeted Lipidomics Data
Jennifer E. Kyle
8. Overview of Tandem Mass Spectral and Metabolite Databases for Metabolite Identification in Metabolomics
Zhangtao Yi and Zheng-Jiang Zhu
9. METLIN: A Metabolite Mass Spectral Database
J. Rafael Montenegro-Burke, Carlos Guijas, and Gary Siuzdak
10. Metabolomic Data Exploration and Analysis with the Human Metabolome Database
David S. Wishart
11. De Novo Molecular Formula Annotation and Structure Elucidation using SIRIUS 4
Marcus Ludwig, Markus Fleischauer, Kai Duhrkop, Martin A. Hoffmann, and Sebastian Boecker
12. Annotation of Specialized Metabolites from High-throughput and High-resolution Mass Spectrometry Metabolomics
Thomas Naake, Emmanuel Gaquerel, and Alisdair R. Fernie
13. Feature Based Molecular Networking for Metabolite Annotation
Vanessa V. Phelan
14. A Bioinformatics Primer to Data Science, with Examples for Metabolomics W. Stephen Pittard, Cecilia "Keeko" Villaveces, and Shuzhao Li
15. The Essential Toolbox of Data Science: Python, R, Git and Docker W. Stephen Pittard and Shuzhao Li
16. Predictive Modeling for Metabolomics Data
Tusharkanti Ghosh, Weiming Zhang, Debashis Ghosh, and Katerina Kechris
17. Using MetaboAnalyst 4.0 for Metabolomics Data Analysis, Interpretation, and Integration with Other Omics Data Jasmine Chong and Jianguo Xia
18. 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, and Michael Witting
19. Pathway Analysis for Targeted and Untargeted Metabolomics
Alla Karnovsky and Shuzhao Li
20. Application of Metabolomics to Renal and Cardiometabolic Diseases
Casey M. Rebholz and Eugene P. Rhee
21. Using the IDEOM Workflow for LCMS-Based Metabolomics Studies of Drug Mechanisms
Anubhav Srivastava and Darren J Creek
22. Analyzing Metabolomics Data for Environmental Health and Exposome Research Yuping Cai, Ana Rosen Vollmar, and Caroline Helen Johnson
23. Network-based Approaches for Multi-omics Integration
Guangyan Zhou, Shuzhao Li, and Jianguo Xia
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