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Objective: Using Surface enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) analysis of the salivary proteins of breast cancer patients (liver qi stagnation syndrome and deficiency of both liver and kidney yin syndrome), and to determine specific protein marker and establish a salivary protein fingerprint for the differentiation of liver qi stagnation syndrome and deficiency of both liver and kidney yin syndrome in patients with breast cancer. Methods: Fourty-seven saliva samples from breast cancer patients (26 patients were of liver qi stagnation syndrome, 21 patients of deficiency of both live and kidney yin syndrome) were tested using SELDI-TOF-MS to establish diagnostic model of traditional Chinese medicine (TCM) for breast cancer. Results: In these 2 groups, 243 proteins peaks were identified and 33 protein peaks showed significantly statistical difference. A diagnostic model consisting of 2 proteins (mass to charge ratio (M/Z) value was 8087.575 Da and 3378.142 Da respectively) was established and could be used to distinguish liver qi stagnation syndrome and deficiency of both liver and kidney yin syndrome. In 47 breast cancer patients, 25 of liver qi stagnation syndrome were correctly diagnosed, and 21 of deficiency of both liver and kidney yin syndrome were correctly ruled out. The sensitivity is 96.15% (25/26), and specificity 80.95% (17/21). Conclusions: Using SELDI-TOF-MS technique to establish salivary protein fingerprint model for TCM syndrome differentiation of breast cancer can provide a novel method of high specificity and sensitivity for the differentiation of TCM syndromes, and further investigation and application should be performed.