EV protein Corona dataset + R pipeline

Extracellular vesicles (EVs) were isolated from HEK293T cells stably expressing CD63-APEX2 and incubated with mouse plasma to study protein corona formation under inflammatory conditions. Plasma was obtained from C57BL/6J mice treated intraperitoneally with either PBS or LPS (5 mg/kg) 3 hours prior to blood collection.EVs (1 × 10¹¹ particles per condition) were incubated with 100 µL of plasma at 37°C for 30 minutes to allow corona formation. Biotin-phenol (500 µM) and H₂O₂ (1 mM) were then added for 1 minute to initiate APEX2-catalyzed biotinylation of proteins in proximity to the EV surface. The reaction was quenched using a solution of sodium ascorbate (10 mM), Trolox (5 mM), and sodium azide (10 mM).Biotinylated proteins were enriched using streptavidin magnetic beads, digested on-bead with trypsin, and analyzed by LC-MS/MS (Orbitrap Eclipse). Raw data were processed with MaxQuant and filtered to remove contaminants and red blood cell proteins. Differential enrichment analysis was performed using the Limma package in R, with significant hits defined as log₂FC ≥ 1 or ≤ –1 and adjusted <i>p</i> ≤ 0.05. Functional enrichment was conducted using clusterProfiler and ReactomePA.