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Cancer Metab. 2014 Jun 30;2:9. doi: 10.1186/2049-3002-2-9. eCollection 2014.

Decoding the dynamics of cellular metabolism and the action of 3-bromopyruvate and 2-deoxyglucose using pulsed stable isotope-resolved metabolomics.

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Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology/Max-Delbrueck Center for Molecular Medicine, Robert Rossle Street 10, Berlin 13125, Germany.
Present address: Faculté des Sciences, de la Technologie et de la Communication, University of Luxembourg, 162 A, Avenue de la Faïencerie L-1511, Luxembourg, Luxembourg.
Contributed equally



Cellular metabolism is highly dynamic and continuously adjusts to the physiological program of the cell. The regulation of metabolism appears at all biological levels: (post-) transcriptional, (post-) translational, and allosteric. This regulatory information is expressed in the metabolome, but in a complex manner. To decode such complex information, new methods are needed in order to facilitate dynamic metabolic characterization at high resolution.


Here, we describe pulsed stable isotope-resolved metabolomics (pSIRM) as a tool for the dynamic metabolic characterization of cellular metabolism. We have adapted gas chromatography-coupled mass spectrometric methods for metabolomic profiling and stable isotope-resolved metabolomics. In addition, we have improved robustness and reproducibility and implemented a strategy for the absolute quantification of metabolites.


By way of examples, we have applied this methodology to characterize central carbon metabolism of a panel of cancer cell lines and to determine the mode of metabolic inhibition of glycolytic inhibitors in times ranging from minutes to hours. Using pSIRM, we observed that 2-deoxyglucose is a metabolic inhibitor, but does not directly act on the glycolytic cascade.


2-Deoxyglucose; 3-Bromopyruvate; Cancer metabolism; GC-MS; Glycolysis; Metabolomics; Stable isotope labeling

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