Overall, our results suggest that the biorelevant assessment of nanoparticle-protein interactions requires a consideration of multiple factors that include both nanoparticle and environmental parameters, the intended route of administration for nanoparticles, and the incubation medium and conditions. Current approaches to the analysis of the nanoparticle protein corona are disruptive in nature, where sample handling steps induce either particle dissociation, agglomeration, and alteration of loosely bound surface proteins (the soft corona) as such we recommend the use of gentle isolation techniques such as field-flow fractionation or in-situ analysis. Furthermore, current sample handling protocols and analytical processes compromise the purpose of surface modification of nanoparticles. As shown from the results, the surface modified (amine-modified, carboxylate-modified) nanoparticles are more monodisperse with a higher number concentration before incubation as measured by PTA. However, upon exposure to protein-containing medium the functionalised particles (particularly amine) show a more significant change in particle size and size distribution. In comparison, unmodified particles appear more stable following protein corona formation in terms of particle size and size distribution.