Deep plasma proteome profiling by enrichment of extracellular vesicles

This work show that enrichment of extracellular vesicles by ultracentrifugation increases the plasma proteome depth by an order of magnitude. Following the enrichment protocol, more than two thousand proteins can routinely be quantified reproducibly by label-free quantification and data independent acquisition (DIA) in single-shot LC-MSMS runs of less than one hour. The project also present an optimized workflow for plasma proteomics that enables high-throughput with very short chromatographic gradients analyzing hundred samples per day with deep proteome coverage, especially when including study-specific spectral libraries generated by repeated injection and gas-phase fractionation of pooled samples