Fig 1: Workflow. a 3-mm sections of frontal cortex or bilateral hippocampi were collected from matched pairs of wildtype and mutant littermates. b P2 fractions were prepared to enrich for synaptic proteins. Shown here is typical enrichment of Homer1, PSD95, and NMDAR1 in P2 fractions, compared to equal amounts of total protein (by BCA assay) from brain homogenate (HO), P1 membrane pellet, and S2 soluble protein. c A panel of IP beads, each conjugated to a different antibody, is incubated with lysate, probed with fluorophore-conjugated antibodies, and read on a flow cytometer. d Known protein-protein interactions among the targeted protein network, in mouse, from the BioGRID database. Red lines indicate IP-western interactions, black lines IP-mass spectrometry. e, f Example histograms and corresponding node-edge visualizations. e Reduced IP: Shank3 Probe: Shank3 in a Shank3B-/- animal. Blue loop on Shank3 indicates a negative log2FC of an IP_Probe for the same target. f Increased Homer_PSD95 in VPA cortex lysate (red) and matched wildtype littermate control (black). Red line between nodes indicates positive log2FC of an interaction