Data files

Contains time series metabolomics measurements in mM from different experiments. Measurements of these internal metabolites should be combined with Growth curve A measurements forthe external metabolites. Contains mean and standard deviation for a few but not all mutants based on multiple time series experiments carried out over the years. Daniel 3rd experiment data is the most complete and is together with Wodke and Tobias measurements used as training data for the model.

Contains for all samples, mean metabolite concentration and shows enzyme concentration used in model fitting and simmulations. Only metabolite present in the model are shown.

Simulation of double mutants and perturbations and time series samples using for Sample 1 only OE mutants of which we update the enzyme concentrations. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model. Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.

Comparison of model SS metabolite concentrations with measured values using 1000x sampling from the Gausian distribution of the measured values based on multiple replicates per measured conditions. Graphs showing the distribution of measured and simulated metabolite concentration for 95 mutand (KO, OE), perturbation and time series measurements. Model simulations performed using 24h proteomics with modification of enzyme parameters for KO and OE mutants.

Contains: -Relative metabolite measurements at different time points from all experiments -Absolute metabolite measurements for amino-acid analysis of the proteome and the cytosol -Effect on adding CaCl2, KCl or NaCl to the medium on growth -Effect of spiking of growth medium with additional amino acids

Contains all 10 parameter sets, loaded with proteomics measurements for three time points (6h,24h, 48h). Contains all parameter sets exported from COPASI, an overview of the parameter sets in the three conditions and how well they perform as well as scripts to load parameter sets as well as an R script to generate an overview of the model error in predicting for all 10 parameter sets.