We collected 102 treatment-naive Nasopharyngeal Carcinoma (NPC) tumors and 62 normal adjacent tissues (NATs) from Chinese patients and conducted multi-level proteomic analysis. A mass spectrometry (MS)-based label-free quantification strategy was adopted for this study. Proteomic and glycoproteomic approaches were carried out on all of the 102 tumors and 62 NATs. Phosphoproteomic analysis was performed on 101 tumors and 53 NATs.