Comparative Proteomic Profiling of Oral Squamous Cell Carcinoma Versus Normal Oral Mucosa to Identify Novel Diagnostic Biomarkers Using Mass Spectrometry

AbstractBackground: Oral squamous cell carcinoma (OSCC) constitutes more than 90% of oral malignancies and carries a persistently poor five-year survival rate owing to late-stage diagnosis. Tissue-based proteomic profiling offers a systematic route to discovering molecular signatures that distinguish malignant from normal oral epithelium.Aim: To identify differentially expressed proteins between OSCC tissue and matched adjacent normal oral mucosa using liquid chromatography tandem mass spectrometry (LC–MS/MS), and to evaluate candidate proteins as potential diagnostic biomarkers.Methods: A case-control proteomic study was performed on fresh-frozen tissue from 20 histologically confirmed OSCC cases and 20 matched normal mucosal biopsies. Proteins were extracted by filter-aided sample preparation (FASP), digested with trypsin, and quantified by label-free quantitation (LFQ) on an Orbitrap Exploris 480. Bioinformatics analysis used MaxQuant/Perseus, with pathway enrichment by Gene Ontology and KEGG. Targeted validation was performed by parallel reaction monitoring (PRM) on three candidate proteins in an independent subset (n = 20).Results (Hypothetical): Approximately 3,120 proteins were identified at 1% FDR. Differential expression analysis revealed 120 significantly upregulated and 95 downregulated proteins (|log􀀀FC| ≥ 1.5, adjusted p < 0.05). Top candidates included LAMC2, S100A8, and PDIA3. PRM validation confirmed all three with AUCs of 0.92, 0.88, and 0.85, respectively. Enriched pathways included extracellular matrix remodeling, epithelial–mesenchymal transition, and antigen processing.Conclusion: Proteomic profiling reveals a robust panel of OSCC-associated proteins with diagnostic potential. Prospective validation in larger, independent cohorts and integration with clinical variables are required before clinical translation.