The Digestion Of Proteins
The digestion of proteins starts in the stomach.

The enzymes that break down proteins can be divided into exopeptidases and endopeptidases. Endopeptidases beak peptide links (the bonds which hold amino acids together) in the middle of polypeptide chains. Exopeptidases break the peptide links of the amino acids at the ends of the chains.
In the gastric pits of the stomach chief cells produce the protein pepsinogen. Oxyntic cells in the gastric pits produce hydrochloric acid . Pepsinogen is inactive but it is converted to the active enzyme pepsin by the action of hydrochloric acid. Pepsin is an endopeptidase that breaks down proteins into shorter polypeptide chains. The mucus produced by the goblet cells helps to prevent the enzyme digesting the stomach wall.
The next stage of the beak down of proteins takes place in the duodenum. Pancreatic juice contains trypsinogen, which is the inactive form of the enzyme trypsin. The wall of the intestine produces enterokinase (another enzyme) which converts trypsinogen to trypsin. Trypsin is a endopeptidase which, like pepsin, proteins and long polypeptide chains into short polypeptide chains.
The pancreatic juice and intestinal juice contains a number of other peptidases. Many of these are exopeptidases, by breaking amino acids from the ends of the shorter polypeptide chains formed by the endopeptidases they complete the digestion of proteins. The enzymes in the intestinal juice are made mainly by secretory cells crypts of Lieberkühn. At least this is what the older text books say!
Recent evidence suggests that the final digestion of di and tripeptides takes place on the cell membrane of the intestinal epithelium, with some enzymes involved being intrinsic proteins in the cell membrane. It suggests that in fact their are no enzymes actually secreted in the intestinal juice. These enzymes in the cell membranes would be classified as exopeptidases