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OBJECTIVE:To evaluate the global changes of salivary protein profiles in patients with systemic sclerosis (SSc) using a proteomic approach. METHODS: Whole saliva (WS) was collected from 15 patients with diffuse SSc and 15 healthy volunteers. Protein expression profiles for each sample were generated by 2-dimensional gel electrophoresis, and protein spots of interest were identified using peptide mass fingerprinting. RESULTS: The level of all the most representative salivary proteins except keratin 6L remained unchanged and only qualitative differences were observed between control subjects and patients with SSc. A total of 19 spots were found in SSc that were not matched with the controls. Fourteen out of a total of 19 spots were identified by mass analysis and were found to collapse into 9 unique proteins. These spots were identified to be cyclophilin A, calgranulin B, psoriasin, beta2-microglobulin, calgranulin A, glyceraldehyde-3-phosphate dehydrogenase, triose phosphate isomerase (TPI), actin-related protein 2/3 complex subunit 2 (Arp2/3 complex), and cystatin B. CONCLUSION: Our study is the first reporting the WS protein pattern of patients with SSc and comparing the differences between WS of patients with SSc and WS of healthy subjects. Both previously identified and newly identified proteins were detected in WS using a proteomic approach. Some of these proteins, like keratin 6L, psoriasin, TPI, and Arp2/3 complex, might have a pathological significance for SSc. It is possible that some of them can be defined as new therapeutic targets or diagnostic markers for SSc disease.