Direct protein analysis from complex cellular samples is crucial for understanding cellular diversity and disease mechanisms. Here, we explored the potential of SiNx solid-state nanopores for single-molecule protein analysis from complex cellular samples. Using the LOV2 protein as model, we designed a nanopore electrophoretic driver protein and fused it with LOV2, thereby enhancing the capture efficiency of the target protein. Then, we performed ex-situ single-cell protein analysis by directly extracting the contents of individual cells using the glass nanopipette-based single-cell extraction and successfully identified and monitored the conformational changes of the LOV2 protein from single-cell extracts using SiNx nanopores. Our results reveal significant differences between proteins measured directly from single cells and those obtained from purified samples. This work demonstrates the potential of solid-state nanopores as a powerful tool for single-cell, single-molecule protein analysis, opening avenues for investigating protein dynamics and interactions at the cellular level.
