An All-in-Tip Accelerated Proteomics Platform for Large-Scale Cancer Screening

Large-scale plasma proteomics studies advance the human proteome atlas mapping and precision medicine, but face inefficiencies in sample processing. Here, we developed a fully automated, room-temperature All-in-Tip platform, enabling deep proteome profiling (>3000 protein groups per batch), high throughput (>4600 samples per day for sample preparation), and low cost (<$1 per sample). The All-in-Tip utilized functional macroporous nanoparticles (NPs) as tip fillings, forming protein corona to narrow the dynamic range of plasma proteomics within 5 min. Additionally, the spatial confinement of NPs accelerated protein digestion to 5 min without excessive enzymes. The All-in-Tip platform demonstrated high reproducibility with the Pearson correlation greater than 0.91 and the median coefficient of variation below 20% for both intrabatch and interbatch analyses. In a pilot study of 190 lung adenocarcinoma samples, our platform identified over 5100 proteins and distinguished malignant from benign pulmonary nodules with areas under the curve (AUC) values of 0.87-0.89. This rapid, in-depth, and high-throughput platform holds promise for expediting cancer screening by enabling the discovery of disease biomarkers and elucidation of their underlying mechanisms from large-scale clinical cohorts.