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The circadian generator is a nucleus, called the suprachiasmatic nucleus (SCN). The neurons of this nucleus contain \u201cclock genes,\u201d the transcription of which exhibits a circadian rhythm. Most circadian rhythms are generated by the neurons of this nucleus and, via neuronal and humoral connections, the SCN controls circadian activity of the brain and peripheral tissues. The endogenous oscillator of the SCN is each day entrained to the length of the daily photoperiod by light that reach the retina, and specialized photoreceptors transmit impulses to the SCN via the optic nerves. Mass screening for day\/night variations in gene expression in the circadian system as well as in the whole brain and peripheral tissues have, during the last decade, been performed. However, studies of circadian changes in the proteome have been less investigated. In this survey, the anatomy and function of the circadian\u2010generating system in mammals is described, and recent proteomic studies that investigate day\/night changes in the retina, SCN, and pineal gland are reviewed. Further circadian changes controlled by the SCN in gene and protein expression in the liver are discussed. \u00a9 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:313\u2013325, 2010<\/jats:p>","DOI":"10.1002\/mas.20237","type":"journal-article","created":{"date-parts":[[2009,5,12]],"date-time":"2009-05-12T16:16:20Z","timestamp":1242144980000},"page":"313-325","source":"Crossref","is-referenced-by-count":7,"title":["Proteomics of the photoneuroendocrine circadian system of the 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