High-throughput plasma/serum proteomics by coupling nanoparticle protein corona-based sample preparation and capillary zone electrophoresis-tandem mass spectrometry

A high-throughput workflow for bottom-up proteomics (BUP) of human plasma using capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) and nanoparticle protein corona-assisted sample preparation is presented. The streamlined approach enabled the identification and quantification of hundreds of proteins from plasma/serum samples in 3.5 hours from sample to data. Nanoparticles with varied physiochemical properties studied in this work captured different pools of the plasma/serum proteome in the protein coronas, and the protein corona-based sample preparation approach enabled the measurement of low-abundance proteins compared to the approach without nanoparticles. Applying this high-throughput workflow to serum samples of a mouse NUT carcinoma (NC) cancer model allowed the determination of differentially expressed serum proteins between NC bearing mice and healthy controls. By comparing our quantitative proteomics data with published transcriptomics data, we revealed a handful of potential serum protein biomarkers of NC cancer (<i>e.g.</i>, secreted phosphoprotein 1, SPP1). We expect this high-throughput workflow, with additional improvement in the speed of the mass spectrometer, will be useful for advancing the discovery of new protein biomarkers of diseases (<i>e.g.</i>, cancer) using plasma/serum samples.