In order to conduct a comparative proteomics study of human nasopharyngeal carcinoma (NPC) to understand the molecular mechanisms that participate in the formation of NPC, the two-dimensional gel electrophoresis (2-DE) reference map of human NPC tissue proteome was described. To provide a high level of reproducibility between gels and accurately array each protein expressed in NPC tissue proteome, the two-dimensional polyacrylamide gel electrophoresis system, modified colloidal Coomassie Brilliant Blue staining method and ImageMaster 2D Platinum image analysis software were used. The NPC 2-DE maps show that high quality and good reproducibility of the 2-DE gel pattern was attained. An average total of 1,100 protein spots were separated by 2-DE, visualized by a modified colloidal Coomassie Brilliant Blue staining method. A synthesized 2-DE reference gel was acquired after detailed analysis of the NPC 2-DE gel maps, and 216 medium to high abundant spots were identified as landmark spots of NPC 2-DE gel, which expressed on >75% of gels. To provide an unambiguous identification of the landmark spots in gels, MALDI-TOF, ESI-Q-TOF mass spectrometry and database search were used to identify the proteins expressed in NPC tissue proteome. Between the 216 landmark spots, all proteins were identified with MALDI-TOF at first, 41 of which were identified with both MALDI-TOF and ESI-Q-TOF. All identified proteins were classified in terms of their subcellular localization and physiological function with information from SWISS-PROT and NCBI websites. According to our knowledge this is the first 2-DE reference map of human NPC. This reference map will serve as a basis for further studies of human NPC and the reference map data will be used to expand the proteome database of human NPC, which can be accessed in our website http://www.xyproteomics.org/.

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