Protein denaturation for in-depth serum proteome profiling and enhanced cancer diagnosis

The in-depth blood-based proteomics is significantly limited owing to the intrinsic wide dynamic range of protein concentrations (over 10 orders of magnitude) and highly abundant proteins (albumin, etc.) in blood. Here, we developed a protein denaturation strategy to enhance the serum proteomic depth via nanoparticle-protein corona for enhanced non-small cell lung cancer (NSCLC) diagnosis. We developed an optimal denaturant panel consists of nature, 30 % acetonitrile, 40 % RapiGest, and 4 M urea respectively treated serum to form various nanoparticle-protein coronas with magnetic nanoparticles (MNPs). Based on this panel, we have identified 1846 proteins by profiling 172 NSCLC serum samples, significantly enhancing the depth of serum proteomics. Furthermore, we selected 15 key proteins with random forest algorithm to distinguish the benign and malignant nodules and achieved an ROC-AUC of 98.44 %. Differentially expressed protein-based pathway analysis revealed that metabolic and immune-related pathways were significantly enriched, in which apolipoproteins play pivotal role in the transfer from benign to malignant nodules. Our study demonstrated a facile serum denaturation strategy for enhanced depth of serum proteomics which will benefit the cancer biomarker discovery and diagnosis.