Background: Proteomic characterization of microglia has been limited by low yield and contamination by non-microglial proteins in magnetic-activated cell sorting (MACS) enrichment strategies. To determine whether a fluorescence-activated cell sorting (FACS)-based strategy overcomes these limitations, we compared microglial proteomes of MACS and FACS-isolated CD11b+ microglia in order to identify core sets of microglial proteins in adult mouse brain tissue. Results: Quantitative multiplexed proteomics by tandem mass tag mass spectrometry (TMT-MS) of MACS-enriched (N = 5) and FACS-isolated (N = 5) adult wild-type CD11b+ microglia identified 1,791 proteins, of which 953 were differentially abundant, indicating significant differences between both approaches. While the FACS-isolated microglia proteome was enriched with cytosolic, endoplasmic reticulum and ribosomal proteins involved in protein metabolism and immune system functions, the MACS-enriched microglia proteome was enriched with proteins related to mitochondrial function and synaptic transmission. As compared to MACS, the FACS microglial proteome showed strong enrichment for canonical microglial proteins while neuron, astrocyte, and oligodendrocyte proteins were depleted. We identified a core set of proteins highly abundant in microglia including Msn and Cotl1 which were validated in immuno-histochemical studies. By comparing FACS-isolated microglia proteomes with transcriptomes, we observed highly concordant as well as highly discordant proteins that were abundant at the protein level but low at the transcript level. Conclusions: We demonstrate that TMT-MS proteomics of FACS isolated adult mouse microglia is superior to column-based enrichment approaches, resulting in purer and more highly-enriched microglial proteomes. We also define core sets of highly-abundant adult microglial proteins that can guide future studies. Key words: microglia, proteomics, mass spectrometry, FACS, MACS