THE HARC CENTER: HIV ACCESSORY AND REGULATORY COMPLEXES PROTEOMICS CORE SUMMARY The Proteomics Core will support all HARC Center Projects by applying and developing mass spectrometry (MS)-based proteomic technologies for the functional and structural characterization of HIV-host protein complexes. Together with the Genetics, Structural Biology, and Computational Cores, we provide a systematic pipeline for the structure determination of Vif-, Tat-, and Rev-host protein complexes. This novel HARC endogenous protein structure (HEPS) platform will collect and integrate structural data to build comprehensive structural models of endogenously purified virus-host complexes. The Proteomics Core will perform endogenous protein purifications and map protein-protein interactions (PPIs) of HIV and host proteins in HIV-infected and genomically edited and unedited primary CD4+ T cells by affinity-purification MS. We will additionally provide structural proteomics methodologies, including native MS (nM); cross-linking (XL)-MS, and hydrogen/deuterium exchange-MS (H/DX-MS), to support the structure determination of challenging and flexible HIV-host protein complexes. Finally, to characterize changes to chromatin and RNA-binding proteins involved in HIV transcription and latency, we will identify and quantitatively compare post-translational modifications (PTMs) of wild-type (WT) and genomically modified CD4+ primary cells infected with WT or mutant HIV.