Discovery of Breast Cancer Diagnostic Markers Using Lipase-Based Plasma Proteomics of Lipid-Bound Proteins

Membrane-associated proteins, including those embedded in exosomal membranes or bound to plasma lipids, are promising disease biomarkers. However, their hydrophobic nature limits detection through conventional proteomic workflows, which primarily capture soluble proteins. In this study, we developed and optimized a lipase-based pretreatment strategy to improve the detection of insoluble membrane proteins in human plasma. Lipase treatment using porcine pancreas-derived enzymes was optimized to 37°C, 3 U, and 1 h, based on overall protein yield and membrane protein enrichment. Sequential application after depletion of high-abundance proteins increased the proportion of membrane proteins from 12%-20%. Using this optimized workflow, we performed data-independent acquisition-based LC-MS/MS analysis of plasma samples from patients with early-stage breast cancer and benign disease (n = 6 each). Notably, 38% of the uniquely detected or enriched proteins in cancer plasma were membrane-associated. Among them, protocadherin 12 (PCDH12) was significantly elevated in the plasma of patients with breast cancer, indicating its potential as a novel diagnostic biomarker. This study highlights the use of lipase-enhanced proteomics for revealing plasma membrane proteins and advancing noninvasive biomarker discovery for cancer.