Technical Assessment on Proteonano: A Robust Platform for Deep Plasma Proteomics Study

Complete profiling of human plasma proteome is an immerse source for disease biomarker discovery. Cutting-edge mass spectrometers, like ThermoFishers Orbitrap Astral, have promised unprecedented insights into the exploration of multiple protein biomarkers from human plasma samples. However, large-scale, deep profiling of the human plasma proteome, especially low-abundant proteins (LAPs, <10 ng.mL- 1), in a robust and fast way remains challenging. This is largely due to the lack of standardized and automated workflows including LAPs enrichment, reduction, and enzymatic digestion procedures. Until now, these complex procedures have not been incorporated into a streamlined workflow to achieve reproducibility, high-throughput, and deep proteome coverage. Here we report the Proteonano Ultraplex Proteomics (PUP) Platform for large cohort plasma proteomics studies with robustness and fast throughput by standardizing workflow by incorporating the Proteonano platform and high-resolution mass spectrometers, including Orbitrap Exploris 480, Orbitrap Astral, and timsTOF Pro. This pipeline demonstrates excellent stability and reproducibility, with tunable balance between proteome coverage and throughput. We further demonstrate the utility of this platform for potential biomarker discovery in a neurodegenerative disease cohort. This harmonized method enables robust, fast and large-cohort plasma proteomics studies to meet the need to discover new biomarkers.