caa a22 4500 528785230 20200328032311.0 cr unu---uuuuu 180924e200508 xx s 000 0 eng 10.3929/ethz-a-005046458 doi 10.1186/1471-2105-6-209 doi (ETHRESEARCH)oai:www.research-collection.ethz.ch:20.500.11850/287426 FiatFlux - a software for metabolic flux analysis from ¹³C-glucose experiments [Elektronische Daten] [Eliane Fischer, Uwe; id_orcid 0000-0002-5923-0770 Sauer] Open access ethresearch Background Quantitative knowledge of intracellular fluxes is important for a comprehensive characterization of metabolic networks and their functional operation. In contrast to direct assessment of metabolite concentrations, in vivo metabolite fluxes must be inferred indirectly from measurable quantities in 13C experiments. The required experience, the complicated network models, large and heterogeneous data sets, and the time-consuming set-up of highly controlled experimental conditions largely restricted metabolic flux analysis to few expert groups. A conceptual simplification of flux analysis is the analytical determination of metabolic flux ratios exclusively from MS data, which can then be used in a second step to estimate absolute in vivo fluxes. Results Here we describe the user-friendly software package FiatFlux that supports flux analysis for non-expert users. In the first module, ratios of converging fluxes are automatically calculated 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. Conclusion FiatFlux is an intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the software to their specific scientific interests, including other 13C-substrates, labeling mixtures, and organisms. Creative Commons Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0 ethresearch STOFFWECHSELWEGE UND STOFFWECHSELZYKLEN (BIOCHEMIE) ethresearch ZELLMETABOLISMUS + ZELLERNÄHRUNG (CYTOLOGIE) ethresearch GLUKOSE (BIOCHEMIE) ethresearch KOHLENSTOFFISOTOPE ethresearch GLUKOSE (BIOCHEMIE) ethresearch BIOLOGISCHE INFORMATIK UND COMPUTERANWENDUNG IN DER BIOLOGIE ethresearch METABOLIC PATHWAYS + METABOLIC CYCLES (BIOCHEMISTRY) ethresearch CELL NUTRITION + CELL METABOLISM (CYTOLOGY) ethresearch GLUCOSE (BIOCHEMISTRY) ethresearch CARBON/ISOTOPES ethresearch GLUCOSE (BIOCHEMISTRY) ethresearch BIOLOGICAL INFORMATICS AND COMPUTER APPLICATIONS IN BIOLOGY ethresearch Flux Ratio ethresearch Flux Analysis ethresearch Metabolic Flux Analysis ethresearch Central Carbon Metabolism ethresearch Ratio Module ethresearch Life sciences ethresearch Fischer Eliane joint author Sauer Uwe; id_orcid 0000-0002-5923-0770 joint author BMC Bioinformatics London : BioMed Central 6, p. 209 1471-2105 http://hdl.handle.net/20.500.11850/287426 text/html WWW-Backlink auf das Repository (Open access) 1 Journal Article ethresearch ETHRESEARCH 856 40 http://hdl.handle.net/20.500.11850/287426 text/html WWW-Backlink auf das Repository (Open access) ETHRESEARCH 700 1- Fischer Eliane joint author ETHRESEARCH 700 1- Sauer Uwe; id_orcid 0000-0002-5923-0770 joint author ETHRESEARCH 773 0- BMC Bioinformatics London : BioMed Central 6, p. 209 1471-2105 BK010053 XK010053 XK010000 ETHRESEARCH ETHRESEARCH ETHRESEARCH Journal Article Open access