The whole saliva is a esoteric watery fluid secreted by the major salivary gland, along with other minor glands. Study of the saliva proteome is beneficial for the understanding of the oral environment physiology and contribute to corresponding diseases diagnosis and prognosis. For urine and saliva proteome analysis, proteins were digested without depletion of abundant proteins and then analyzed by 2DLC-MS/MS. The high-resolution tandem mass spectra, were searched against Swissprot database and then imported into Scaffold software to ensure the false-positive rates for protein. Protein identification were controlled to less than 1% and each protein had at least two unique peptides.