A system for combinatorial deposition of a thin layer on a substrate is described. The system comprises at least one deposition material source holder and a substrate holder. The system also comprises a rotatable positioning system for subsequently positioning the at least one substrate in parallel and in non-parallel configuration with at least one deposition material source. The system comprises at least one mask holder arranged for positioning a mask between at least one of the target holder and the positioning system, for allowing variation of the material flux across the at least one substrate when the combinatorial deposition is performed. The mask holder is in a fixed arrangement with respect to the at least one deposition material source holder during the combinatorial depositing.