Replication Data for: Cell cycle-dependent protein dynamics in budding yeast resolved by deconvolution of bulk proteomics

Because bulk proteomics of synchronised cell populations is inherently blurred by progressive desynchronisation, we developed a model-based deconvolution method — combining a yeast population model with a regularised least-squares algorithm — to reconstruct underlying single-cell concentration dynamics from population-level measurements.

Applying this to time-course proteomics data from elutriation-synchronised cultures (3373 quantified proteins), we identified 563 proteins with higher-confidence cell cycle-dependent dynamics, many consistent with known yeast cell cycle biology. The dataset includes these deconvolved trajectories along with the underlying raw and processed proteomics, cell volume, and cell cycle phase distribution data, and associated model code, as a resource for studying the dynamic processes coordinating cell growth and division.