List of Chapters

1. Overview of experimental methods and study design in metabolomics, and statistical and pathway considerations

Stephen Barnes, Ph.D

Department of Pharmacology & Toxicology and Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294

2. Metabolomics data processing using XCMS

Xavier Domingo-Almenara a* , Gary Siuzdak a,b

a Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States. b Department of Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

Link to software: https://bioconductor.org/packages/release/bioc/html/xcms.html

3. Metabolomics data processing using MzMine and ADAP

Xiuxia Du,∗,† Aleksandr Smirnov,† Tomáš Pluskal,‡ Wei Jia¶, and Susan Sumner§

†University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States ‡Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States ¶University of Hawaii Cancer Center, Honolulu, Hawaii 96813, United States §University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States

Link to software: http://mzmine.github.io/

4. Metabolomics data processing using OpenMS

Marc Rurik1, Oliver Alka1, Fabian Aicheler1, and Oliver Kohlbacher1,2,3,4

1 Applied Bioinformatics Group, University of Tubingen, Tubingen, Germany 2 Biomolecular Interactions, Max Planck Institute for Developmental Biology,Tubingen, Germany 3 Quantitative Biology Center, University of Tubingen, Tubingen, Germany 4 Institute for Translational Bioinformatics, University Hospital Tubingen, Tubingen, Germany

Link to software: https://www.openms.de/

5. Analysis of NMR Metabolomics Data

Wimal Pathmasiri, Kristine Kay, Susan McRitchie, and Susan Sumner

NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081, USA.

6. Key concepts surrounding studies of stable isotope resolved metabolomics.

Stephen F. Previs, PhD and Daniel P. Downes, PhD Department of Chemistry Merck & Co., Inc. Kenilworth, NJ, USA 2000 Galloping Hill Road, K15-MW111 Kenilworth, NJ 07033 USA

Richard Higashi, PhD Professor & Director of Mass Spectrometry Center for Environmental & Systems Biochemistry University of Kentucky, Lexington KY, U.S.A.

7. Extracting Biological Insight from Untargeted Lipidomics Data

Jennifer E. Kyle, Ph.D

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA

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

Zhangtao Yi and Zheng-Jiang Zhu

Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China

9. METLIN: A Metabolite Mass Spectral Database

J. Rafael Montenegro-Burke, Carlos Guijas, Gary Siuzdak

Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.

Link to database: https://metlin.scripps.edu/

10. Metabolomic Data Exploration and Analysis with The Human Metabolome Database

David S. Wishart

Department of Computing Science; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8

Link to database: http://www.hmdb.ca/

11. De novo molecular formula annotation and structure elucidation using SIRIUS 4

Marcus Ludwig, Markus Fleischauer, Kai Du ̈hrkop, Martin A. Hoffmann and Sebastian Bocker

Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany

Link to software: https://bio.informatik.uni-jena.de/software/sirius/

12. Annotation of specialized metabolites from high-throughput and high-resolution mass spectrometry metabolomics

Thomas Naake 1 , Emmanuel Gaquerel 2,3 , Alisdair R. Fernie 1

1 Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany 2 Institute of Plant Molecular Biology, CNRS UPR 2357, University of Strasbourg, F-67000 Strasbourg, France 3 Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany

Link to software MetNet MetCir

13. Feature Based Molecular Networking for Metabolite Annotation

Vanessa Phelan, Ph.D

Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA

Link to software GNPS

Example data can be accessed via the GNPS menu option ‘MassIVE Datasets’ via accession number MSV000083500, at https://massive.ucsd.edu

14. A bioinformatics primer to data science, with examples for metabolomics

W Stephen Pittard, Cecilia Villaveces, Shuzhao Li

1 Department of Biostatistics and Bioinformatics, 2 Department of Medicine, Emory University, Atlanta, Georgia, USA. GA 30322.

Link to notebooks

15. The essential tool set for data science: Python, R, Git and Docker

W. Stephen Pittard 1 and Shuzhao Li 2,*

1 Department of Biostatistics and Bioinformatics, 2 Department of Medicine, Emory University, Atlanta, Georgia, USA. GA 30322.

16. Predictive Modeling for Metabolomics Data

Tusharkanti Ghosh, Weiming Zhang, Debashis Ghosh and Katerina Kechris

Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America

Link to notebooks

17. Using MetaboAnalyst 4.0 for metabolomics data analysis, interpretation and integration with other omics data

Jasmine Chong 1 and Jianguo Xia 1,2

1 Institute of Parasitology, McGill University, Montreal, Quebec, Canada 2 Department of Animal Science, McGill University, Montreal, Quebec, Canada

Link to software: https://www.metaboanalyst.ca/

18. Using genome scale metabolic networks for analysis, visualization, and integration of targeted metabolomics data

Jake. P. N. Hattwell [1], Janna Hastings [2], Olivia Casanueva [2], Horst Joachim Schirra [1], Michael Witting [3][4]

[1] The University of Queensland, Centre for Advanced Imaging, Brisbane, Qld 4072, Australia [2] Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom [3] Helmholtz Zentrum München, Research Unit Analytical BioGeoChemistry, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [4] Technical University of Munich, Chair of Analytical Food Chemistry, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany

Link to repository

19. Pathway analysis for targeted and untargeted metabolomics

Alla Karnovsky 1 and Shuzhao Li 2

1 Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA. MI 48109. 2 Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA. GA 30322.

Link to software MetScape Mummichog

20. Application of Metabolomics to Renal and Cardiometabolic Disease

Casey M. Rebholz (Johns Hopkins University),

Eugene P. Rhee (Massachusetts General Hospital)

21. Using the IDEOM workflow for LCMS-based metabolomics studies of drug mechanisms

Anubhav Srivastava and Darren J Creek

Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.

22. Analyzing Metabolomics Data for Environmental Health and Exposome Research

Yuping Cai, Ana Rosen Vollmar and Caroline Helen Johnson*

Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA

23. Network-based Approaches for Multi-omics Integration

Guangyan Zhou 1 , Shuzhao Li 2 and Jianguo Xia 1,3,4,5

1 Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Quebec, Canada H9X 3V9 2 Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA GA 30322 3 Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada H9X 3V9 4 Department of Microbiology and Immunology, and 5 Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 2B4