The term “proteome” was first used in 1995 by Wilkins et al. to describe the protein complement to the genome. Hence proteomics can be defined as the large scale study of protein properties such as expression level, post translational modifications and interactions with other molecules to obtain a global view of cellular processes at the protein level. At present the most suitable approach towards this goal is separation and visualization of proteins from crude tissue extracts by two-dimensional gel electrophoresis (2-DE) followed by the identification and characterization of the isolated proteins by mass spectrometric techniques. Two-dimensional gel electrophoresis used to study abiotic stress in plants such as: drought, salinity, high and low temperature and presence of toxic chemicals such as herbicide and toxic heavy metals. These types of studies in which proteins are extracted from cells under different conditions and elucidate the difference in proteome are so-called “protein differential display” analysis. Such analysis nowadays used to address the effect of physiological and environmental factors in a range experimental situation from the formation of human cancer to mechanism of cellular prcess in plants. In the present study comparative analysis of seed and leaf proteins was done in germination process and cooper treatment respectively. For these purpose at first protein extraction from these tissue were optimized using five protein extraction protocol follow five lysis buffers. In germination process lots of spots were upregulated in germinated seeds among them seven spots were identified using mass spectrometry (MS/MS).in continues the effect of copper on pomegranate leaf proteome was investigated. For this, pomegranate seedlings in MS medium was sprayed with copper sulfate. After two dimensional gel electrophoresis of leaf proteins, two spots that upregulated in treated seedlings were identified using MS\MS. Furthermore seed storage proteome analysis with SDS-PAGE show ten bonds. In continues two dimensional gel electrophoresis of seed proteins show that one of these bonds have nine isoforms and others have two isoforms finally among them three bonds were identified using MS\MS. Also we showed that all of pomegranate seed storage proteins have inter or intra disulfide bond this led to a complex pattern of storage proteins in seed. To our knowledge this is the first recorded proteomics study on pomegranate