Bread wheat (Triticum aestivum ssp. aestivum) is an economically important cereal crop grown worldwide. It contributes to human diet providing a high nutritional value and its unique rheological characteristics enable a diverse range of food end-products. However, some wheat proteins can cause adverse health reactions. In this study, LC-MS based label-free quantitative proteomics was performed to characterize the (water/salt-extractable) flour proteome of 150 hexaploid wheat cultivars grown under three different environmental conditions. 114 of 756 proteins were found to be stably expressed across the different environments. They were detected in more than 50 % of cultivars in three environments and showed a high heritability (H² > 0.6). The complete set of cultivars was genotyped and a genome scan using 22,220 DArTseq markers was performed and allowed to identify a total of 63 major QTLs with a high proportion of explained genetic variance (11%-84%) for 54 proteins. A total of 21 QTLs controlling glutens and potential allergenic proteins were identified, of which three QTLs were associated with only two gluten proteins, five QTLs were underpinning common proteins between glutens and allergens, and eight QTLs were associated with only allergenic proteins. Among the 21 QTLs, three were detected on chromosomes 1A, 1B and 1D near known glutenin genes and two QTLs, located on chromosomes 5A and 5B, were found to be linked with major genes expressing lipid transfer proteins. Summarizing, potential molecular markers for marker assisted selection were identified for 54 proteins enabling the design of qualitatively better wheat varieties in the future.