Main description:

This detailed volume focuses on recent technological, computational, and biostatistical advances in the field of high-throughput metabolomics. Chapters encompass methods, platforms, and analytical strategies for steady state measurements and metabolic flux analysis with stable isotope-labeled tracers, in biological matrices of clinical relevance and model organisms. Mass spectrometry-based or orthogonal methods are discussed, along with computational and statistical methods to address data sparsity in high-throughput metabolomics approaches. As a part of the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, High-Throughput Metabolomics: Methods and Protocols provides tools that can bring about the next generation of clinical biochemistry in a cost-effective, rigorous fashion, exponentially advancing our capacity to investigate nature while hastening the advent of personalized medicine.

Contents:

Part I: Methods

1. Sample Preparation and Reporting Standards for Metabolomics of Adherent Mammalian Cells

Sarah Hayton, Robert D. Trengove, and Garth L. Maker

2. High-Throughput Metabolomics: Isocratic and Gradient Mass Spectrometry-Based Methods

Travis Nemkov, Julie A. Reisz, Sarah Gehrke, Kirk C. Hansen, and Angelo D'Alessandro

3. High-Throughput Metabolomics Based on Direct Mass Spectrometry Analysis in Biomedical Research

Raul Gonzalez-Dominguez, Alvaro Gonzalez-Dominguez, Carmen Segundo, Monica Schwarz, Ana Sayago, Rosa Maria Mateos, Enrique Duran-Guerrero, Alfonso Maria Lechuga-Sancho, and Angeles Fernandez-Recamales

4. Traveling Wave Ion Mobility Mass Spectrometry: Metabolomics Applications

Giuseppe Paglia and Giuseppe Astarita

5. CE-MS for Metabolomics: A Comparison with Other Techniques

Joanna Godzien, Antonia Garcia, Angeles Lopez-Gonzalvez, and Coral Barbas

Part II: Lipidomics

6. Overview of Lipid Mass Spectrometry and Lipidomics

Simona Zarini, Robert M. Barkley, Miguel A. Gijon, and Robert C. Murphy

7. LC-MS/MS-MRM-Based Targeted Metabolomics for Quantitative Analysis of Polyunsaturated Fatty Acids and Oxylipins

Xiaoyun Fu, Mikayla Anderson, Yi Wang, and James C. Zimring

8. Untargeted and Semi-Targeted Lipid Analysis of Biological Samples Using Mass Spectrometry-Based Metabolomics

Julie A. Reisz, Connie Zheng, Angelo D'Alessandro, and Travis Nemkov

9. HPLC-MS/MS Methods for Diacylglycerol and Sphingolipid Molecular Species in Skeletal Muscle

Kathleen A. Harrison and Bryan C. Bergman

Part III: Metabolomics of Animal and Plant Models

10. Quantification of D- and L-2-Hydroxyglutarate in Drosophila melanogaster Tissue Samples Using Gas Chromatography-Mass Spectrometry

Hongde Li and Jason M. Tennessen

11. Comprehensive LC-MS-Based Metabolite Fingerprinting Approach for Plant and Fungal-Derived Samples

Kirstin Feussner and Ivo Feussner

12. Untargeted Metabolomics of Plant Leaf Tissues

Federica Gevi, Giuseppina Fanelli, Lello Zolla, and Sara Rinalducci

Part IV: Tracing Experiments and Metabolic Flux Analysis

13. Analysis of Arginine Metabolism Using LC-MS and Isotopic Labeling

Gretchen L. Seim, Emily C. Britt, and Jing Fan

14. Quantifying Intermediary Metabolism and Lipogenesis in Cultured Mammalian Cells Using Stable Isotope Tracing and Mass Spectrometry

Thekla Cordes and Christian M. Metallo

15. Insights into Dynamic Network States Using Metabolomic Data

Reihaneh Mostolizadeh, Andreas Drager, and Neema Jamshidi

16. Analysis of Endothelial Fatty Acid Metabolism Using Tracer Metabolomics

Joanna Kalucka, Bart Ghesquiere, Sarah-Maria Fendt, and Peter Carmeliet

17. Using Stable Isotope Tracers for Metabolic Pathway Analysis

Sara Violante, Tiffany H. Thomas, and Justin R. Cross

Part V: Data Processing in Metabolomics

18. Data Processing for GC-MS and LC-MS-Based Untargeted Metabolomics

Linxing Yao, Amy M. Sheflin, Corey D. Broeckling, and Jessica E. Prenni

19. El-MAVEN: A Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics

Shubhra Agrawal, Sahil Kumar, Raghav Sehgal, Sabu George, Rishabh Gupta, Surbhi Poddar, Abhishek Jha, and Swetabh Pathak

20. Pre-Analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data

Dominik Reinhold, Harrison Pielke-Lombardo, Sean Jacobson, Debashis Ghosh, and Katerina Kechris

Part VI: Metabolic Measurements with Techniques Orthogonal to Mass Spectrometry

21. Temporal Metabolite, Ion, and Enzyme Activity Profiling Using Fluorescence Microscopy and Genetically-Encoded Biosensors

Douglas A. Chapnick, Eric Bunker, Xuedong Liu, and William M. Old

22. Microplate Assays for Spectrophotometric Measurement of Mitochondrial Enzyme Activity

Rachel C. Janssen and Kristen E. Boyle

23. Quantitative NMR-Based Metabolomics on Tissue Biomarkers and Its Translation into In Vivo Magnetic Resonance Spectroscopy

Natalie J. Serkova, Denise M. Davis, Jenna Steiner, and Rajesh Agarwal

Part VII: Towards Personalized Metabolomics

24. Metabolomic Applications in Radiation Biodosimetry

Evagelia C. Laiakis

25. Metabolomics Analyses to Investigate the Role of Diet and Physical Training

Pol Herrero, Miguel Angel Rodriguez, M Rosa Ras, Antoni del Pino, Lluis Arola, and Nuria Canela

26. Blood Biomarkers in Sports Medicine and Performance and the Future of Metabolomics

Inigo San Millan

27. Personalized Metabolomics

David P. Marciano and Michael P. Snyder