Research comparing the biochemical composition of wheat grains from organic or conventional agriculture has used the targeted analytical approach. To obtain a more comprehensive record of the food's composition, we employed protein profiling techniques. Levels of 1049 proteins were recorded in wheat grains (Triticum aestivum L., cv. Titlis) of two growing seasons from a rigorously controlled field trial in Switzerland, containing organic and conventional plots. Levels of 25 proteins were different between organic and conventional wheat in both years. Storage proteins, enzymes of carbohydrate metabolism, a peroxidase, and proteins of unknown function were affected by the agricultural regime. Total protein content was lower in organic wheat. We consider these differences negligible with regard to nutrition in an average diet and propose that food quality of conventional and organic wheat grown in the field trial was equal. Applying various filters and calculations, one of which takes seasonal influences into account, 16 of the 25 proteins with different levels in organic and conventional wheat were retained. These 16 "diagnostic" proteins have the potential to afford a signature to prove authenticity of organic wheat.