Fig 1: Enrichment of organellar markers in ATG9 and RAB26 vesicles. (A) box plots showing the enrichments of organelle-specific proteins detected in the ATG9 and RAB26 proteome (see Figure S1 for the respective 2D scatter plots). SV, synaptic vesicles (blue), EL, endosomes and lysosomes (orange), PM, plasma membranes (gray), GA, Golgi apparatus (yellow), ER, endoplasmic reticulum (light blue), Mito, mitochondria (green), Px, peroxisomes (dark blue). The Y-axis shows the average log2-fold enrichment (log2 iBAQ ATG9/Input + log2 iBAQ ATG9/control IgG) divided by 2 of the individual proteins of each group. Bottom: graphs representing the fraction (in %) of the proteins listed in the respective organelle database (see text for details) that were recovered in the respective immuno-isolates (the numbers on top of the bars represent the total number of proteins in the organelle proteomes). (B) distribution of selected proteins between vesicles immuno-isolated for SYP and ATG9, respectively. Immuno-isolated fractions were analyzed by immunoblotting for select proteins, confirming MS-based quantification of proteins enriched in ATG9-containing vesicles. These include TMEM9B, M6PR, LC3B, SNAP23, VTI1A, VAMP7, ATG2A and PIP4K2A found in ATG9-containing vesicles compared to Synpatophysin vesicles. See Figure 1 for details. (C) scatter plot showing the proteins enriched > 2-fold in both dimensions, corresponding to a cutoff of log2-transformed iBAQ (ATG9/Control) and (ATG9/Input) >1, for both ATG9 (red, upper graph) and RAB26 (violet, lower graph). (D) Venn diagram of the > 2-fold enriched proteins in the ATG9 (red) and RAB26 (violet) proteome showing that overlap is limited. (E) as in (C) but limited to the recovered organelle-specific proteins, respectively.