Liquid Chromatography-Tandem Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Head and Neck Squamous Cell Carcinomas

Background: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and one of the malignant tumors with poor prognosis. To gain insights into HNSCC, we analyzed the proteome and phosphoproteome between cancerous and paracancerous normal tissue samples using quantitative mass spectrometry. Methods: Proteins were extracted from five pairs of tumor -normal samples and digested for data -independent acquisition mass spectrometry. Subsequently, phosphopeptides were enriched using TiO2 and prepared for phosphoproteome detection. A bioinformatics analysis was then conducted to identify potential biomarkers for HNSCC. Results: A total of 1239 protein groups and 2025 phosphorylation sites were differentially expressed. Among these, KRT16, MUC21, SH3BGRL2, ASL, and METTL7A were selected as biomarkers for HNSCC. Conclusions: This study presents a comprehensive and quantitative analysis using mass spectrometry of five pairs of NHSCC samples, including five adjacent non -cancerous tissues, unveiling five potential protein biomarkers for HNSCC.