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FiatFlux delivers 13C metabolic flux analysis to non-expert users. Two distinct modules exist. The first calculates ratios of converging fluxes from GC-MS-detected 13C-pattern in protein-bound amino acids. Predefined fragmentation patterns are automatically identified and appropriate statistical data treatment is based on the comparison of redundant information in the MS spectra. In the second module, absolute intracellular fluxes may be calculated by a 13C-constrained flux balancing procedure that combines experimentally determined fluxes in and out of the cell and the above flux ratios. The software is preconfigured to derive flux ratios and absolute in vivo fluxes from [1-13C] and [U-13C]glucose experiments and GC-MS analysis of amino acids for a variety of microorganisms.


Matlab 6.0 or later (tested on Win)
Matlab Optimization Toolbox



  • Fischer and Sauer, Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem. 2003;270(5):880-91 
  • Fischer, Zamboni, and Sauer, High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem. 2004;325(2):308-16 


  • Zamboni, Fischer, and Sauer, FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinformatics. 2005;6:209 
  • Zamboni, Fendt, Rühl, and Sauer, 13C-based metabolic flux analysis, Nat protocols 2009; 4(6):878-892 

Examples of applications:

  • Fischer and Sauer, Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet. 2005;37(6):636-40
  • Fuhrer, Fischer and Sauer, Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol. 2005;187(5):1581-90
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