Cells are continuously exposed to various stresses originating from their own function, environmental changes, and pathogens. To understand the cellular responses to stresses, molecular systems approaches are required to assess and integrate the various global and molecular changes. Quantitative proteomics has proven particularly powerful to directly monitor underlying changes in protein abundance and modifications.

We focus on applying quantitative proteomics to study stress responses, such as proteostasis perturbation and host-pathogen interactions. To be able to determine the highly dynamic and time resolved effects of stresses, we develop proteomics tools capable of resolving these conditions. Therefore, we focus on approaches that combine pulse-SILAC labeling with tandem mass tag-multiplexing. I will present multiplexed enhanced protein dynamics (mePROD) proteomics that allow to globally monitor protein translation and will show examples of its use to understand cellular translatome changes upon inhibition of the integrated stress response and mTORC1 – two crucial cellular stress hubs. Then I will present data from cells infected with SARS-CoV-2. The use systems biology approaches focusing on multi-level proteomics allowed us to first predict and then validate a number of drugs that prevent SARS-CoV-2 replication in cells and have now moved towards the clinic.

Overall, I will give an overview over novel approaches to measure protein dynamics by proteomics including the required bioinformatics tools for their analyses. I will provide examples of the strength of these methods in studying cellular protein dynamics during stress and infection.