The human gastric mucosa is the most active layer of the stomach wall, involved in food digestion, metabolic processes and gastric carcinogenesis. Anatomically, the human stomach is divided into seven regions, but the protein basis for cellular specialization is not well understood. Here we present a global analysis of protein profiles of 82 apparently normal mucosa samples obtained from living individuals by endoscopic stomach biopsy. We identify 6,258 high-confidence proteins and estimate the ranges of protein expression in the seven stomach regions, presenting a region-resolved proteome reference map of the near normal, human stomach. Furthermore, we measure mucosa protein profiles of tumor and tumor nearby tissues (TNT) from 58 gastric cancer patients, enabling comparisons between tumor, TNT, and normal tissue. These datasets provide a rich resource for the gastrointestinal tract research community to investigate the molecular basis for region-specific functions in mucosa physiology and pathology including gastric cancer.