Deep proteomic analysis of human microglia and model systems reveal fundamental biological differences ofin vitroandex vivocells

Using high resolution quantitative mass spectrometry we have generated in-depth proteome maps of human and mouseex vivoandin vitromicroglia. We reveal a tenfold difference in protein content ofex vivoandin vitrocells and fundamental differences in protein expression related to protein synthesis, metabolism, microglia markers and environmental sensors. While human and mouse microglia are different in their proteomes, the species differences are smaller than the changes induced by cell culture. Remarkably, xenografting human microglia derived from human stem cells into mouse brain restores thein vivo-like microglia proteomic signature including reduction in the total amount of protein, energy demand and protein synthesis, and re-expression of homeostatic microglia markers. We identify more than 9000 microglia proteins and discuss how they relate to microglia function. This data provides a vital proteomic resource for understandingin vitroandex vivomicroglia phenotypes.