A Se-targeted bottom-up proteomics approach was developed for the identification of Se-containing proteins in rice grown naturally on seleniferous soils. The proteins were separated by 2D gel electrophoresis. The position of Se-containing spots was tentatively identified by the correlation between the 1D isoelectrofocusing (IEF) and 1D SDS electropherograms of a sample aliquot and confirmed by (78)Se imaging in the 2D gel. The method was complemented by the ICP-MS assisted shotgun proteomics approach. The proteins were identified by capHPLC with the dual ICP MS and electrospray Orbitrap MS detection. The first ever comprehensive study of rice selenoproteome revealed the presence of selenium, as both selenomethionine (SeMet) and selenocysteine (SeCys) residues, in a dozen proteins including a 19 kDa globulin, granule-bound starch synthase, and the family of glutelin-type seed storage proteins.