Global, quantitative and dynamic mapping of protein subcellular localization

TLDR

Subcellular localization determines protein function and is tightly regulated to control cellular processes. The authors developed Dynamic Organellar Maps, a proteomic approach for global mapping of protein translocation events. Dynamic Organellar Maps generate static proteomic maps of over 8,700 HeLa proteins, then track dynamic translocations after EGF stimulation by integrating spatial and abundance data into a quantitative model. The approach resolves all major organelles with >92% accuracy, yields a quantitative view of HeLa cell anatomy, and captures dynamic protein movements, enabling proteome‑wide analysis without process‑specific reagents.

Abstract

Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.