This project contains label-free LC–MS/MS proteomic data from particle-associated protein fractions isolated after cellular uptake of non-targeted nanoparticles (NP) or F-actin-targeting Art-myosin. Cultured cells were exposed to NP or Art-myosin for 2 h, washed to remove non-internalized particles, lysed and subjected to magnetic separation. The recovered proteins were analysed in three biological replicates per group. This dataset was generated to compare proteins associated with NP and Art-myosin and to investigate cytoskeletal, mechanotransduction, endocytic and intracellular-trafficking pathways.