Proteomic Evidence Indicates Ultrasound-Assisted Extraction Enhances Recovery of Membrane-Associated Proteins in Hericium erinaceus

), and the proteins were fractionated by molecular weight (≥30 kDa, 10-30 kDa, 3-10 kDa). Proteomic profiling using data-dependent (DDA) and data-independent (DIA) mass spectrometry identified 1500 and 1702 proteins, respectively (1% global FDR). Ultrasonication induced surface irregularity and a less compact, heterogeneous microstructure. Topology predictions showed higher proportions of transmembrane and secretory proteins in ultrasonicated fractions. Extraction preserved protein integrity (82% molecular-weight retention, 97% tryptic specificity, 26:1 stable-to-degraded ratio). The ≥30 kDa fraction was enriched for the endomembrane system and cytoskeletal components; the 10-30 kDa fraction captured mitochondrial respirasome and vacuolar V-ATPase complexes; the 3-10 kDa fraction contained mainly cytosolic proteins. Ultrasonication-unique proteins showed higher aromaticity, and abundant ≥ 30 kDa proteins displayed membrane-proximal characteristics.