Fig. 1: Quantitative proteomic and phosphoproteomic analysis of the cell cycle in RPE-1 cells.
A General experiments workflow of cell synchronisation coupled to MS analysis. Cells were arrested in late G1 with palbociclib (Palbo) and time points corresponding to different cell cycle phases were collected upon release from the inhibitor. Sample aliquots were fixed and DNA was stained with propidium iodide for flow cytometry. For MS analysis, cells were lysed and protein digested with trypsin, followed by TMT labelling and phosphopeptide enrichment. B Flow cytometry analysis assessing DNA content at each time point. C Principal component analysis of the log2 mean normalised abundances (Supplementary Data 2) for each replicate from each time point from the proteomic data. Colour represents time point. Replicates are labelled in each circle. The loading (i.e. how much each original sample contributes to each principal component) are available in Supplementary Data 1. D Principal component analysis of the phosphoproteome, as described for (C). The loading (i.e. how much each original sample contributes to each principal component) are available in Supplementary Data 1. E Comparative analysis of our proteomics data with previously published cell cycle studies5,6,7,8,9,15. For each dataset, the coverage of the human proteome (based on the 20,377 UniProt reviewed human proteins) and the number of proteins associated with the Gene Ontology (GO) term ‘mitotic cell cycle process’ detected are listed. Cyclins identified in each study are shown with circles.
