Chaotropic Surface Chemistry for Protein Profiling with Solid-State Micropores

Proteins derive their biological identity from an amino acid sequence, and even subtle sequence variations can mark disease states, therapeutic response, and cancer progression. Although solid-state nanopores offer single-molecule sensitivity, protein analysis with conventional nanopores remains limited by stochastic capture, rapid translocation, and the need for sub-nanometer control over pore dimensions. Here, we report that this size-matching requirement can be bypassed by converting sequence-dependent protein surface chemistry into amplified particle-scale transport signatures through leveraging chaotropic chemistry for surface charge modulation. We immobilized monoclonal anti-prostate-specific antigen antibody variants, differing only in partial amino acid sequence, on polymeric microparticles and measured their passage through readily fabricated SiN x micropores. In the presence of guanidine hydrochloride, chaotropic perturbation of hydration shells and compression of the electric double layer reshaped the electrokinetic landscape around the particle–protein complexes in a variant-dependent manner. These chemically amplified differences generated distinct resistive pulse waveforms, allowing near-perfect discrimination of antibody variants by machine learning. This approach shifts protein sensing from geometrical confinement in nanoscale pores to chemically tuned amplification in micrometer-scale pores, providing a scalable route to sequence-sensitive biomarker profiling without advanced nanofabrication.