The circadian clock in the retina regulates a variety of physiological phenomena 
such as disc shedding and melatonin release. Although these events are critical 
for retinal functions, it is almost unknown how the circadian clock controls the 
physiological rhythmicity. To gain insight into the processes, we performed a 
proteomic analysis using 2-DE to find proteins whose levels show circadian 
changes. Among 415 retinal protein spots, 11 protein spots showed circadian 
rhythmicity in their intensities. We performed MALDI-TOF MS and NanoLC-MS/MS 
analyses and identified proteins contained in the 11 spots. The proteins were 
related to vesicular transport, calcium-binding, protein degradation, 
metabolism, RNA-binding, and protein foldings, suggesting the clock-regulation 
of neurotransmitter release, transportation of the membrane proteins, 
calcium-binding capability, and so on. We also found a rhythmic phosphorylation 
of N-ethylmaleimide-sensitive fusion protein and identified one of the amino 
acid residues modified by phosphorylation. These findings provide a new 
perspective on the relationship between the physiological functions of the 
retina and the circadian clock system.