With the development of proteomics mass spectrometry and intelligent algorithm, using intelligent algorithm to analysis clinical mass spectrum data had showed a good application prospect in the tumor early diagnosis. Based on the study of MATLAB Builder JA Toolbox and intelligent algorithms which are used to analyze protein mass spectrum data, and combing with JavaEE technology, we design and achieve a tumor diagnosis web platform based on protein mass spectrum. The platform mainly achieves three big functions which are mass spectrum data visualization display, intelligent matching and intelligent diagnosis algorithm. While still providing patients' basic information and tumor data management, mass spectrometry biological characteristics site settings and the analysis results data storage such as additional functions.