Abstract

In the past two decades, metabolic flux analysis with stable isotopic tracers has been the method of choice to investigate cellular metabolism. A variety of labeling strategies and computational frameworks have been devised and used to quantify the motion of metabolites through the biochemical network in simple systems, i.e. microbial networks. In parallel, the metabolomics community has made major progresses in densely, sensitively, precisely, and yet rapidly profiling cellular metabolites in cells and their environment. Unfortunately, the interpretation of metabolome profiles remains a largely heuristic process. Both approaches have reached an impressive level of sophistication and are in a phase of technical consolidation. 

Starting from the strengths and weaknesses of these approaches, I discuss strategies on how to unravel metabolic responses and the underlying regulation in cultured cells. For complex metabolic systems, I demonstrate the general superiority of non-targeted, dynamic metabolomics experiments and advocate for a sporadic, selective use of targeted 13C-metabolic flux analysis.