Abstract: Objective To explore the differentially expressed protiens of the tumor tissues of nasopharyngeal carcinoma (NPC) primary focus in different clinical types including upward progressing type，downward progressing type and mixed progressing type. Methods The total proteins of tissues from normal nasopharyngeal mucosa and NPC in different clinical types were separated by two-dimensional electrophoresis (2-DE), then proteins spots were analyzed and the differentially expressed proteins were identified by matrix assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF-MS) combined with bioinformatics analysis. Results Thirty-one significant differentially expressed proteins between mixed progressing type of NPC and normal tissues were found. And among of them, 18 proteins were up-regulated and 13 proteins were down-regulated in mixed type of NPC. Five proteins of ten differential expressed proteins selected from mixed progressing type of NPC were identified by MALDI-TOF-MS. Heat shock cognate 71 kDa protein，alpha-1-antitrypsin and macrophage-capping protein were up-regulated and Protein S100A9 and Protein 4.1 were down-regulated in mixed progressing type of NPC as compared with those in normal nasopharyngeal mucosa tissues. Thirty-one significant differentially expressed proteins between upward and downward progressing types of NPC were also found. And among of them, 15 proteins were up-regulated and 16 proteins were down-regulated in upward progressing type of NPC as compared with those in downward progressing type of NPC. Six proteins of ten differential expressed proteins selected from upward progressing types of NPC were identified by MALDI-TOF-MS. Mitochondrial aconitate hydratase , alcohol dehydrogenase [NADP+] and Rab GDP dissociation inhibitor beta were up-regulated and NM23-H1, nuclear chloride channel-27 and aldehyde dehydrogenase X were down-regulated in upward progressing type of NPC as compared with those in downward progressing type of NPC. Conclusion There were significant differences at proteins related to tumor metastasis, energy metabolism，retoxity and anti-metastasis between different clinical type of NPC. These proteins may be as markers of clinical types of NPC.

Key words: Nasopharyngeal carcinoma, Clinical types, Proteomics, Mass spectrometry, difference