13C-based metabolic flux analysis

摘要: The quantitative analysis of metabolic fluxes, i.e., in vivo activities intracellular enzymes and pathways, provides key information on biological systems biology engineering. It is based a comprehensive approach combining (i) tracer cultivation 13C substrates, (ii) labelling by mass spectrometry (iii) mathematical modelling for experimental design, data processing, flux calculation statistics. Whereas the analytical part fairly advanced, lack appropriate software solutions all aspects studies limiting application analysis. We have developed OpenFLUX as user friendly, yet flexible small large scale new Elementary Metabolite Unit (EMU) framework significantly enhancing computation speed calculation. From simple notation reaction networks defined spreadsheet, parser automatically generates MATLAB-readable metabolite isotopomer balances, thus strongly facilitating model creation. can be used to perform parameter estimation sensitivity either using built-in gradient-based search or Monte Carlo algorithms userdefined algorithms. Exemplified microbial study allowed very user-friendly fashion compile EMU-based from an Excel file containing reactions carbon transfer mechanisms. reliably reproduced published optimum distributions network under were found quickly (<20 sec). fast, accurate steady-state will facilitate enhance interpretation studies. By providing open source, we hope it evolve with rapidly growing field fluxomics. (1) Quek, L.E., C. Wittmann, L.K. Nielsen, J.O. Kromer, (2009). OpenFLUX: efficient 13C-based Microbial cell factories. 8: p. 25.