Subcellular proteomic profiling of human skeletal muscle reveals exercise-induced coordinated and compartment-specific protein remodeling

This repository contains R scripts supporting the analyses presented in the manuscript “Subcellular proteomic profiling of human skeletal muscle reveals exercise-induced, compartment-specific protein remodelling across mitochondrial, nuclear and cytosolic compartments.” The code includes preprocessing and normalisation workflows for mitochondrial, nuclear, and cytosolic fractions, differential expression and enrichment analyses, implementation of the mitochondrial protein enrichment (MPE) correction strategy, cross-compartment integration and visualisation, as well as modules for physiological (training) data and western blot quantification (including RACK1-focused analyses). Scripts are structured to be run sequentially and are organised by subcellular fraction prior to integration.