Objective To compare the proteomic profiles of whole unstimulated saliva（WUS） of subjects with chronic periodontitis（CP） with that of healthy volunteers, and to identify proteins. Methods WUS was obtained from five subjects with CP and five healthy subjects, and proteins were separated using two-dimensional gel electrophoresis（2-DE）. Proteins, the level of which was significantly different among the two groups, were identified by computer image analyses and subsequent matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry（MALDI-TOF-TOF MS）. Results Seventeen differentially expressed points in the 2-DE gel between the two samples were found by professional software. And protein types of thirteen points were then identified. Among them, the point 737, 725, 692, 986 was the same protein, as well as the point 716, 535. They were respectively serum albumin; β-fibrin; chain B, human serum transferrin, recombinant N-terminal lobe, Apo form, crystal form 2; Ig alpha-1 chain C region; the GA module complexed with human serum albumin（HAB-GA）; chain B, crystal structure of a Rca-Rhogdi complexes; PRO2044; hypothetical protein; unnamed protein. Compared with whole saliva of healthy control subjects, the levels of them were increased in whole unstimulated saliva of CP subjects. Conclusion Comparison of the proteomic profiles of WUS of CP subjects with that of healthy control subjects reveals at least 9 differential proteins. The approach might be helpful to better understand to the etiology of CP.
