Immunogenic gluten peptides trigger Celiac Disease (CD), an adaptive immune response in genetically predisposed individuals. Given the structural similarity between all gluten proteins their individual CD influence is not clear. Hence, the extraction, separation and characterization of wheat gluten proteins have become relevant to measure their individual potential immunoreactivity. Wheat proteins were extracted from commercial wheat flour and further isolated by preparative HPLC. The resulting richest gliadin sub-fractions were characterized by nano-LC-MS/MS following a shotgun proteomic approach in order to identify the prolamins in the original commercial wheat flour. It was found that the gliadin extract was additionally composed of glutenins and avenin-like proteins. Accurate prolamin identification has emerged as a need to delve deep into the influence of each fraction on the onset of celiac disease. After protein characterization, the immunoreactivity towards the main epitope related to CD was verified by ELISA and western blotting for several different gluten fractions.