Proteome and phophoproteome analysis of distinct dendritic cell maturation states

Depending on their environment and their exposure to various factors, dendritic cells (DCs) exist in different activation and maturation states. The versatility of DCs allows them to shape the immune system towards an inflammatory or tolerant state depending on the antigens and the environment they encounter. In this study we aimed to provide a proteomic catalogue of differentially expressed and differentially phosphorylated proteins between distinct DC maturation states, brought about by bacteria that differ in their endotoxicity. To achieve this, we have performed unlabeled shotgun proteomics and phosphoproteomics on cell fractions obtained from murine bone marrow DC cultures. The symbiont B. vulgatus stimulation was used to obtain semi-mature DCs, and the pathobiont E. coli stimulation was used to obtain mature DCs. For both shotgun proteome and phosphoproteome analysis two biological replicates consisting of 8 mice were used. Each biological replicate were run as 3 technical replicates.