SELDI-TOF-MS of 10-200 kDa peaks revealed 8 peaks with >2-fold changes in the SS group that differed from non-SS (p< 0.005). Peaks of 11.8, 12.0, 14.3, 80.6 and 83.7 kDa were increased, while 17.3, 25.4, and 35.4 kDa peaks were decreased in SS samples. 2D-DIGE identified significant ↑ of β2-microglobulin, lactoferrin, immunoglobulin (Ig) kappa light chain, polymeric Ig receptor, lysozyme C and cystatin C in all stages of SS. Two presumed proline-rich proteins, amylase and carbonic anhydrase VI, were ↓ in the patient group. Here, CA6 is linked to synovial sarcoma.