Information on the files related to the respective experiments can be found in the metadata file titled “Metadata_for_Nviennensis_Carbon_Experiment.xlsx”. The ammonia-oxidizing archaeon Nitrososphaera viennensis was subjected to various levels of carbon limitation based on predictions from a thermodynamic model. Catalase or pyruvate was used as a reactive oxygen species scavenger. A combined extraction of proteins and metabolites was performed in each condition to evaluate the cellular response to carbon limitation. The proteomic data associated with the project can be found here.