Rab2- and VMAT-specific PB-MS results, and colocalization of ILP2-GFP and TurboID-VMAT in motor neuron soma and synaptic bouton. (A) Previously identified Rab2 effectors (both Drosophila proteins and mammalian orthologs) found in our screen to be significantly enriched in TurboID-Rab2^Q65L samples relative to TurboID-Rab2^S20N. First 14 entries, confirmed effectors (also labelled in Fig. 1 B). All subunits of the HOPS complex were counted as effectors. Last 5 entries, potential effectors detected by affinity proteomics in Drosophila S2 cells (Gillingham et al., 2014) and MitoID relocalization proximity proteomics in HEK cells (Gillingham et al., 2019) but not confirmed using other methods. The list of unconfirmed effectors is not exhaustive. (B) Proteins known to reside on DCVs or to be involved in DCV biogenesis that were significantly enriched in TurboID-VMAT samples relative to free TurboID. (C) Representative STED images showing the distribution of ILP2-GFP and TurboID-HA-VMAT in motor neuron cell body located in the dorsomedial aspect of the VNC (left) and in peripheral synaptic bouton (right) in a third instar larva. White arrowheads, TurboID-VMAT associated with ILP-GFP–positive DCVs. Blue arrowheads, small TurboID-VMAT–positive vesicles not associated with ILP-GFP. The distribution of ILP2-GFP and TurboID-HA-VMAT in the mid-axon region in the same type of preparation is shown in Fig. 1 D. Scale bars (left to right): 1µm, 400 nm (inset 1), 200 nm (inset 2), 400 nm, 200 nm (inset).