Utilizing tandem mass spectrometry for metabolic flux analysis

Abstract

Metabolic flux analysis (MFA) aims at revealing the metabolic reaction rates in a complex biochemical network. To do so, MFA uses the input of stable isotope labeling patterns of the intracellular metabolites. Elementary metabolic unit (EMU) is the computational framework to simulate the metabolite labeling patterns in a network, which was originally designed for simulating mass isotopomer distributions (MIDs) at the MS1 level. Recently, the EMU framework is expanded to simulate tandem mass spectrometry data. Tandem mass spectrometry has emerged as a new experimental approach to provide information on the positional isotope labeling of metabolites and therefore greatly improves the precision of MFA. In this review, we will discuss the new EMU framework that can accommodate the tandem mass isotopomer distributions (TMIDs) data. We will also analyze the improvement on the MFA precision by using TMID. Our analysis shows that combining the MIDs of the parent and daughter ions and the TMID for the MFA is more powerful than using TMID alone.

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Fig. 1: Tandem mass spectrometry data.
Fig. 2: Fragmentation pathways of malate.
Fig. 3: Gluconeogenesis network model including TCA cycle and glyoxylate shunt.
Fig. 4: Comparison of flux uncertainty.

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Acknowledgements

This research is supported, in part, by NIH grants P30CA072720-5923 (XS) and R00DK117066 (SH).

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Correspondence to Xiaoyang Su.

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Wang, Y., Hui, S., Wondisford, F.E. et al. Utilizing tandem mass spectrometry for metabolic flux analysis. Lab Invest (2020). https://doi.org/10.1038/s41374-020-00488-z

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