High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells

Camilla Rega, Ifigenia Tsitsa, Theodoros I. Roumeliotis, Izabella Krystkowiak, Maria Portillo, Lu Yu, Julia Vorhauser, Jonathon Pines, Jörg Mansfeld, Jyoti Choudhary and Norman E. Davey ()
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Camilla Rega: The Institute of Cancer Research
Ifigenia Tsitsa: The Institute of Cancer Research
Theodoros I. Roumeliotis: The Institute of Cancer Research
Izabella Krystkowiak: The Institute of Cancer Research
Maria Portillo: The Institute of Cancer Research
Lu Yu: The Institute of Cancer Research
Julia Vorhauser: The Institute of Cancer Research
Jonathon Pines: The Institute of Cancer Research
Jörg Mansfeld: The Institute of Cancer Research
Jyoti Choudhary: The Institute of Cancer Research
Norman E. Davey: The Institute of Cancer Research

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract The cell cycle governs a precise series of molecular events, regulated by coordinated changes in protein and phosphorylation abundance, that culminates in the generation of two daughter cells. Here, we present a proteomic and phosphoproteomic analysis of the human cell cycle in hTERT-RPE-1 cells using deep quantitative mass spectrometry by isobaric labelling. By analysing non-transformed cells and improving the temporal resolution and coverage of key cell cycle regulators, we present a dataset of cell cycle-dependent protein and phosphorylation site oscillation that offers a foundational reference for investigating cell cycle regulation. These data reveal regulatory intricacies including proteins and phosphorylation sites exhibiting cell cycle-dependent oscillation, and proteins targeted for degradation during mitotic exit. Integrated with complementary resources, our data link cycle-dependent abundance dynamics to functional changes and are accessible through the Cell Cycle database (CCdb), an interactive web-based resource for the cell cycle community.

Date: 2025
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DOI: 10.1038/s41467-025-57537-8

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