Enhanced Competition at the Nano–Bio Interface Enables Comprehensive Characterization of Protein Corona Dynamics and Deep Coverage of Proteomes

Abstract Introducing engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle–protein interface, driven by the relationship between protein–NP affinity and protein abundance. This enables scalable systems that leverage protein–nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Here the importance of the protein to NP‐surface ratio (P/NP) is demonstrated and protein corona formation dynamics are modeled, which determine the competition between proteins for binding. Tuning the P/NP ratio significantly modulates the protein corona composition, enhancing depth and precision of a fully automated NP‐based deep proteomic workflow (Proteograph). By increasing the binding competition on engineered NPs, 1.2–1.7× more proteins with 1% false discovery rate are identified on the surface of each NP, and up to 3× more proteins compared to a standard plasma proteomics workflow. Moreover, the data suggest P/NP plays a significant role in determining the in vivo fate of nanomaterials in biomedical applications. Together, the study showcases the importance of P/NP as a key design element for biomaterials and nanomedicine in vivo and as a powerful tuning strategy for accurate, large‐scale NP‐based deep proteomic studies.