Comparison of soluble vacuolar proteins. (a) Normalized heavy/light ratios for all soluble vacuolar proteins in isolated vacuoles across the different mutants were analyzed (error bars show the SD from 3 to 4 measurements). (b) Normalized heavy/light ratios for all soluble vacuolar proteins in whole cell extracts across the different mutants analyzed. (c) Sorting of AP-3 cargoes according to their binding motifs. Transmembrane proteins were divided into groups with the tyrosine motif, dileucine motif, or both according to their amino acid sequence. Only cytosolic parts were counted (according to Uniprot database). (d) Comparison of protein ratios from vacuole samples of two experiments, APM3 D217A G469K versus APM3. Proteins with a dileucine motif are colored in red, proteins bearing a tyrosine motif in blue, and proteins with both motifs in purple. The asterisks indicate non–TM proteins. (e) Comparison of protein ratios from vacuole samples of two experiments, APS3 V106D L121S versus APS3. Known AP-3 cargoes are colored in red and cargoes identified in our screen colored in blue. The asterisks indicate non–TM proteins. (f) Vacuolar proteomics of the AP-3 cargo Atg27. atg27Δ cells show a significant decrease in CVT cargo proteins and Atg8 in isolated vacuoles in comparison to WT cells.