Wheat seed proteins were studied to identify the cultivar–specific proteins using two Korean pre-harvest sprouting wheat cultivars; Jinpum (susceptible) and Keumgang (resistant). Wheat seed proteins were separated by two-dimensional electrophoresis with IEF gels over pH ranges: pH 3.5-10. A total of 73 spots were digested with trypsin resulting peptide fragmentation were analyzed by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/MS). Mass spectra were automatically processed and searched through NCBInr, SWISS-PORT and MSDB database with mono isotopic masses. These proteins profiles are divided into 9 categories: Metabolism, Storage, Photosynthesis, Amino Acid, Allergy, Stress, Protein Synthesis, Enzyme and, Hypothetical protein. The gluten includes two different components, high molecular weight glutenin subunits and low molecular weight glutenin subunits and gliadins. Some selected protein spots were detected to be (i) gluten, which is responsible for roughness and viscoelasticity for bread making quality (ii) stress proteins (biotic and abiotic) associated with salt, cold, heat tolerance, disease (iii) pathogen related proteins, and (iv) allergenic proteins responsible for allergy in humans, (v) puroindoline- a & b (encoding PinA and PinB gene)that is responsible for grain texture related to baking performance and roughness and other molecular functions such as antibiotic / toxin / antimicrobial activities, that contribute to the defense mechanism of the plant against predators. Moreover, to gain a better understanding of proteome analysis and identify the pre-harvest sprouting responsible proteins, we carried out a comparative proteomic analysis in pre-harvest sprouting wheat seeds between susceptible and resistant cultivars.