IsoDesign: A Software for Optimizing the Design of 13C-Metabolic Flux Analysis Experiments

The growing demand for C-13-metabolic flux analysis (C-13-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming C-13-labeling experiments. Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. We present IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to C-13-MFA investigations using a broad panel of analytical tools (MS, MS/MS, H-1 NMR, C-13 NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. Applications of IsoDesign are described, with an example of the entire C-13-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of C-13-MFA experiments more accessible to a wider biological community. IsoDesign is distributed under an open source license at http://metasys.insa-toulouse.fr/software/isodes/ Biotechnol. Bioeng. 2014;111: 202-208. (c) 2013 Wiley Periodicals, Inc.