Updated project metadata. To dissect how diurnal rhythms affect key functions such as transcription or chromatin remodelling, we quantified the temporal nuclear accumulation of proteins and phosphoproteins from mouse liver using in vivo stable isotope labelling by amino acids in cell culture (SILAC)-based mass spectrometry (MS). Protein extracts from isotope labelled mice liver nuclei were used as a reference and mixed with extracts from animals collected every 3 h for 45 h total. Phosphopeptide levels were analysed after enrichment with titanium dioxide (TiO2). The proteins levels were also analysed (dataset with project accession PXD003818).