We conducted a large-scale identification of protein degradation under light or dark condition in the model cyanobacterium Synechocystis PCC 6803 (Hereafter referred as Synechocystis) using the isobaric labeling based quantitative proteomics technique. This is the first discovery about redox-regulated protein degradation in cyanobacteria. Our results provide the first comprehensive catalog of the light-dependent protein degradation events, and would act as an important resource in future study toward understanding light-regulated processes and protein quality control mechanism in cyanobacteria.