Our work focuses on biomarker discovery in immunological diseases, with particular interest in transplantation immunology and cancer immunology. Approximately 25% of end-stage renal disease patients on the kidney transplant waiting list have alloreactive antibodies in their serum. Using two-dimensional Western blotting experiments followed by mass spectrometry we identified the most common antigens as tubulin beta chain, vimentin, lamin-B1, and Rho GDP-dissociation inhibitor 2. We could show that the antigenicity of these proteins is restricted to specific post-translational modifications. A detailed analysis of vimentin expression revealed that the antigenic 60 kDa isoform is underrepresented in patient’s lymphocytes in comparison to those of healthy volunteers. Lymphocytes of hemodialysis patients showed an expression of vimentin isoforms with a molecular weight between 37 and 49 kDa. Concanavalin A (Con A) activated lymphocytes express a 49 kDa vimentin isoform on their cell surface while the 60 kDa isoform remains inaccessible from the outside. This cell surface expression is associated with an increased binding of sera from hemodialysis patients which were positive for anti-vimentin antibodies. In vitro studies showed that a 49 kDa vimentin fragment is formed during apoptosis by active caspase-3. However, we could not validate any correlation of the 49 kDa vimentin isoform to apoptosis in vivo. Current projects investigate the molecular background of these PTMs.