Integrated Protein Precipitation-Solid-Phase Extraction Workflow for Deep Top-Down Proteomic Analysis of Human Serum

Top-down proteomics of human serum is hindered by extreme dynamic range and cumbersome prefractionation. Here, we establish a fully solution-based protein precipitation-solid-phase extraction (PP-SPE) workflow for deep, low-molecular-weight-biased proteoform profiling. Using systematically optimized combinations of five precipitants and three sorbents, the workflow enabled identification of 4470 proteoforms from 480 proteins with excellent reproducibility (R > 0.96). Compared with the gel-based PEPPI method, PP-SPE provided substantially greater depth, including >10-fold more <5 kDa proteoforms, while shortening the overall sample preparation workflow and offering a format that is readily adaptable to plate-based platforms, thus providing a robust front end for high-throughput serum top-down analyses.