Fig. 2: Defining oscillating protein and phosphorylation events during cell cycle progression.

A Simplified data analysis workflow used to define oscillating proteins and phosphorylation sites. B Scatter plot summarising proteomics results shows the log₂ curve fold change (oscillation score) and the −log10 q-values from the ANOVA test. Significantly oscillating proteins are shown in blue and non-significant proteins are in grey. Dotted lines represent cut-offs used to define oscillating proteins (ANOVA q ≤ 0.01, curve fold change ≥ 1.2). Well-known cell cycle-regulated proteins are highlighted. C Scatter plot summarising phosphoproteomics results shows the fitted log₂ curve fold change and the −log10 q-values from the ANOVA test. Significantly oscillating phosphorylation sites are shown in red and non-significant phosphorylation sites are in grey. Dotted lines represent cut-offs used to define oscillating phosphorylation events (ANOVA q ≤ 0.01, curve fold change ≥ 1.2). Well-known cell cycle-regulated phosphorylation sites are highlighted. D Heatmap showing well-known cell cycle-regulated protein changes during the cell cycle detected by MS. Protein changes are coloured according to their abundance (log₂ mean normalised values). E Western blot validation of the protein changes is shown in (D). F Fisher’s exact test Gene Ontology (GO) analysis of the set of oscillating proteins. The top three significantly enriched terms for each category (Reactome, Biological Processes, Molecular Function and Cellular Components) are shown. G Overlap of the set of oscillating proteins with those detected in other studies. H Heatmap showing well-known cell cycle-regulated CDK1 phosphorylation changes during the cell cycle identified by MS. Phosphorylation changes are coloured according to their abundance (log₂ mean normalised values). I Western blot validation of the phosphorylation changes shown in (H). J Fisher’s exact test Gene Ontology (GO) analysis of oscillating phosphorylation sites. The top three significantly enriched terms for each category (Reactome, Biological Processes, Molecular Function and Cellular Components) are shown. K Overlap of the set of oscillating phosphorylation sites with those detected in other studies. Western blots shown in (E, I) are representative of at least three independent experiments with similar results. Source data are provided as a Source Data file.