title: IsoDesign: a software for optimizing the design of 13C-metabolic flux analysis experiments.
abstract: The growing demand for (13) C-metabolic flux analysis ((13) C-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming (13) C-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 (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C 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 (13) C-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of (13) C-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/
authors.affiliation: MetaSys, Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France; CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Millard
authors.forename: Serguei
authors.initials: S
authors.lastname: Sokol
authors.forename: Fabien
authors.initials: F
authors.lastname: Letisse
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Portais
mesh_terms: D002247:Carbon Isotopes / Q000032:analysis / Q000378:metabolism; D064688:Metabolic Flux Analysis / Q000379:methods*; D019906:Nuclear Magnetic Resonance, Biomolecular; D012107:Research Design; D012984:Software
chemical_list: D002247:Carbon Isotopes
keywords: 13C-metabolic flux analysis; MS; NMR; experimental design; isotope labeling experiments