Metabolic Flux Analysis in Eukaryotic Cells

1. Front Matter

   Pages i-xiii

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2. Determination of Isotopologue and Tandem Mass Isotopologue Ratios Using Gas Chromatography Chemical Ionization Time of Flight Mass Spectrometry - Methodology and Uncertainty of Measurement

   • Teresa Mairinger, Stephen Hann

   Pages 1-16

3. Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes

   • Christian-Alexander Dudek, Lisa Schlicker, Karsten Hiller

   Pages 17-32

4. Liquid Chromatography Methods for Separation of Polar and Charged Intracellular Metabolites for 13C Metabolic Flux Analysis

   • Damini Jaiswal, Anjali Mittal, Deepak Nagrath, Pramod P. Wangikar

   Pages 33-50

5. Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells

   • Esther W. Lim, Seth J. Parker, Christian M. Metallo

   Pages 51-71

6. Large-Scale Profiling of Cellular Metabolic Activities Using Deep 13C Labeling Medium

   • Nina Grankvist, Jeramie D. Watrous, Mohit Jain, Roland Nilsson

   Pages 73-92

7. Analyzing the Metabolism of Metastases in Mice

   • Patricia Altea-Manzano, Dorien Broekaert, João A. G. Duarte, Juan Fernández-García, Mélanie Planque, Sarah-Maria Fendt

   Pages 93-118

8. Robust Analytical Methods for the Accurate Quantification of the Total Biomass Composition of Mammalian Cells

   • Diana Széliová, Harald Schoeny, Špela Knez, Christina Troyer, Cristina Coman, Evelyn Rampler et al.

   Pages 119-160

9. Quantifying Nitric Oxide Flux Distributions

   • Darshan M. Sivaloganathan, Xuanqing Wan, Mark P. Brynildsen

   Pages 161-188

10. SWATH: A Data-Independent Tandem Mass Spectrometry Method to Quantify 13C Enrichment in Cellular Metabolites and Fragments

    • Damini Jaiswal, Pramod P. Wangikar

    Pages 189-204

11. Quantifying Metabolic Transfer Mediated by Extracellular Vesicles Using Exo-MFA: An Integrated Empirical and Computational Platform

    • Abhinav Achreja, Noah Meurs, Deepak Nagrath

    Pages 205-221

12. Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism

    • Sarah McGarrity, Sigurður T. Karvelsson, Ólafur E. Sigurjónsson, Óttar Rolfsson

    Pages 223-269

13. Software Supporting a Workflow of Quantitative Dynamic Flux Maps Estimation in Central Metabolism from SIRM Experimental Data

    • Vitaly A. Selivanov, Silvia Marin, Josep Tarragó-Celada, Andrew N. Lane, Richard M. Higashi, Teresa W.-M. Fan et al.

    Pages 271-298

14. Inferring Metabolic Flux from Time-Course Metabolomics

    • Scott Campit, Sriram Chandrasekaran

    Pages 299-313

15. Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects

    • Kristopher Rawls, Bonnie V. Dougherty, Jason Papin

    Pages 315-330

16. Single-cell Digital Twins for Cancer Preclinical Investigation

    • Marzia Di Filippo, Chiara Damiani, Marco Vanoni, Davide Maspero, Giancarlo Mauri, Lilia Alberghina et al.

    Pages 331-343

17. Supply and Demand Analysis of Autophagy

    • André du Toit, Ben Loos, Jan Hendrik S. Hofmeyr

    Pages 345-357

18. Thermodynamic Approaches in Flux Analysis

    • Sabine Peres, Vincent Fromion

    Pages 359-367

19. Back Matter

    Pages 369-370

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This volume explores the latest metabolic flux analysis (MFA) techniques that cover the analysis of cellular, organ level, and whole-body metabolism. The chapters in this book discuss topics such as deutrium tracing; isotopologue fractions using GC-TOF; non-targeted mass isotopolome analysis; large-scale profiling of cellular metabolic activities using deep 13C labeling medium; metastases in mice; SWATH; Exo-MFA; metabolic flux from time-course metabolomics; and thermodynamic approaches in flux analysis. Written in the highly successful Methods in Molecular Biology series format, 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.
 
Cutting-edge and comprehensive, Metabolic Flux Analysis in Eukaryotic Cells: Methods and Protocols is a valuable resourcefor both experts in MFA techniques and researchers getting involved in the role of quantitative studies to uncover the dysregulated pathways in human diseases.

• lipid metabolism
• Dynamic stable-isotope modeling
• transcriptional regulatory networks
• pSIRM
• Exosome-mediated metabolic flux analysis
• Metabolomics

• Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA

  Deepak Nagrath

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