Integration of proteomics data

[alinarekena]

Hi! Wanted to ask an advice on the integration of proteomics data at STAGE 4. I'm getting an infeasible ecModel at STEP 19 after applying enzyme concentrations. The issue doesn't even allow to update protein pool and load flux data. I tried with adjusting biomass composition (protein/carb, lipid content), but it didn't help. Is there anything major different at this stage now? Because with GECKO 2 the same data worked.

[mihai-sysbio]

Hi @alinarekena! Thanks for giving GECKO3 a try, I remember talking to you about it back at the ME conference.

an infeasible ecModel at STEP 19 after applying enzyme concentrations

Just to confirm, is this just after this line in STEP 19:

ecModel = fillEnzConcs(ecModel,protData);

[alinarekena]

Hi @mihai-sysbio!
No, it occured after this line in STEP 19:
ecModel = constrainEnzConcs(ecModel);