UASt regulatory sequences drive expression of the 'matrix-QC' mitophagy reporter, which consists of the mCherry and GFP coding sequences in tandem and fused to the Tag:Mito(hCOX8A) mitochondrial matrix targeting sequence. Under normal conditions, fluorescence from both mCherry and GFP occurs. Upon mitophagy and incorporation of the mitochondrion into a lysosome, the low pH of the lysosome quenches the GFP signal but not the mCherry signal.