Compartment resolved reference proteome map from highly purified naïve, activated, effector, and memory CD8⁺ murine immune cells

Differentiation of CD8⁺ T lymphocytes into effector and memory cells is key for an adequate immune response and relies on complex interplay of pathways that convey signals from the cell surface to the nucleus. In this study, we investigated the proteome of four cytotoxic T-cell subtypes; naïve, recently activated effector, effector, and memory cells. Cells were fractionated into membrane, cytosol, soluble nuclear, chromatin-bound, and cytoskeletal compartments. Following LC-MS/MS analysis, identified peptides were analyzed via MaxQuant. Compartment fractionation and gel-LC-MS separation resulted in 2399 proteins identified in total. Comparison between the different subsets resulted in 146 significantly regulated proteins for naïve and effector cells, followed by 116 for activated, and 55 for memory cells. Besides Granzyme B signaling (for activated and/ or effector cells vs. naïve cells), the most prominent changes occurred in the TCA cycle and aspartate degradation. These changes suggest that correct balancing of metabolism is key for differentiation processes. All MS data have been deposited in the ProteomeXchange with identifier PXD001065 (http://proteomecentral.proteomexchange.org/dataset/PXD001065).