Nanoparticle Protein Corona Unlocks a Frontier in Deep and Reproducible Host Cell Protein Profiling for Biologics Development

The use of nanomaterials to transform proteomics has reached a critical inflection point with nanoparticle protein coronas being widely applied to explore the plasma, serum, and cerebrospinal fluid proteomes. This inflection was spurred by our introduction of Proteograph, an automated nanoparticle protein corona capture instrument, assay, and software platform. Proteograph XT, the second iteration of the platform, leverages four nanoparticles in a multiplexed format, each with surface chemistry optimized to capture a diverse and distinct set of proteins in their corona. The application of the Proteograph platform to biofluids has been widely published, but to our knowledge, this is the first application of a nanoparticle protein corona workflow to host cell proteins (HCPs) surveillance in a standardized monoclonal antibody reference (National Institute of Standards and Technology (NIST) RM 8671) and an industrial vaccine across eight downstream purification (DSP) stages. Applied to the NIST monoclonal antibody reference material (RM 8671), nanoparticle capture increased HCP identifications by ∼5.5× in data-dependent and ∼4× in data-independent mass spectrometry modes compared with conventional denaturing digestion, without compromising reproducibility or precision (median percentage coefficient of variation (%CV) ≤ 19%). The workflow consistently detected 95 of 101 “problematic” HCPs, including low-parts per million species often invisible to traditional methods. Importantly, these advantages extended to a commercial vaccine biologic, where across eight DSP stages, nanoparticle capture identified ∼2–6× more HCPs at every stage, retaining a ∼6× advantage in late eluates. Together, these results establish nanoparticle protein coronas as a versatile preanalytical tool for deep, reproducible HCP surveillance in both standardized reference materials and manufacturing pipelines. More broadly, this work highlights the extension of nanoscale materials to proteomics beyond human biofluids to de-risk biologics production, accelerate therapeutic development, and embed nanotechnology as a promising tool for next-generation quality control in medicine.