We used proteomics analysis to generate the profiles of proteins in the endosperm and embryo of common buckwheat grains. These differentially expressed proteins are potentially involved in seed metabolism. Extractions were done by trichloroacetic acid (TCA) precipitation. The resulting proteins were separated using SDS-PAGE coupled to LC-ESI-Q/TOF-MS/MS. This allowed us to detect and identify 67 proteins with isoforms, making this the most inclusive protein profile. The proteins were determined to be functionally involved in the central metabolic pathway of the seed, with metabolic interest being reflected in the occurrence of a tissue-specific enzyme balance. For a case in point, we found a tissuespecific and subcellular compartment-specific isoform of granule-bound starch synthase 1 in the chloroplast/amyloplast. This provided proteomic verification of the presence of a distinct regulatory mechanism for the biosynthesis of glycan and starch, which produce amylase and amylopectin. Furthermore, several previously characterized allergenic proteins such as 11S and 13S globulin seed storage protein were acknowledged in our seed samples, thus representing the potential for proteomics techniques that survey food sources for any incidence of allergens. This protein profile of common buckwheat grain is a new avenue for understanding its seed physiology in dormant stage as well as suggesting commercial applications for the buckwheat industry as buckwheat flour.