Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Circulating blood proteomics enables minimally invasive biomarker discovery. Nanoparticle-based circulating plasma proteomics studies have reported varying number of proteins (ca 2000-7000), but it’s unclear whether higher protein number is more informative. Here, we first develop OmniProt – a silica-nanoparticle workflow optimized through systematic evaluation of nanoparticle types and protein corona formation parameters. Next, we present an Astral spectral library for 10,109 protein groups. Using Astral with 60 sample-per-day throughput, OmniProt identifies ca 3000 to 6000 protein groups from human plasma. Notably, platelet/erythrocyte/coagulation-related contamination artificially elevates protein identifications and compromises quantification accuracy in nanoparticle-enriched samples. Through controlled contamination experiments, we identified biomarkers for platelet/erythrocyte/coagulation-related contaminations in nanoparticle-based plasma proteomics. We developed open-access software Baize for contamination assessment. We validated pipeline in 193 patients with CT-indistinct benign nodules or early lung cancers, flagging five contaminated samples. This study reveals contamination alters protein identification/quantification in nanoparticle-based plasma proteomics and presents Baize software to evaluate contamination.