Mouse Circadian Proteome Atlas by next-generation deep proteome analysis

The circadian clock drives daily rhythms of gene expression and physiological functions across tissues throughout the body. Advances in next-generation DNA sequencing have provided extensive insights into gene expression at the RNA level, but more functional information at the protein level with sufficient depth has been limited by technical challenges. Recently, the next-generation mass spectrometer Orbitrap Astral was developed, allowing us to quantify protein abundance with greater sensitivity and accuracy. In this study, we generated a comprehensive mouse circadian proteome atlas (available in URL) by analyzing protein abundance in 32 tissues including the suprachiasmatic nucleus (SCN) across the day using Orbitrap Astral. Data-independent acquisition of 500 samples including developmental samples revealed the spatiotemporal profiles of 18,751 proteins, accounting for 73% of all proteins registered in UniProt. Proteome and phospho-proteome analyses of whole-cell and nuclear proteins in the liver uncovered circadian profiles not only in protein abundance but also in subcellular localization and post-translational modification. Notably, proteome analysis revealed global changes in protein phosphorylation status in hPER2-S662G mutant mice, a genetic model of human familial advanced sleep phase (FASP). This multi-tissue circadian proteome atlas provides a fundamental resource for understanding when, where, and which proteins are expressed and function.