This is correct. With perhaps a few exceptions, your body is not in the business of absorbing whole proteins. Trypsin is one of the enzymes used to reduce pepti

This is correct. With perhaps a few exceptions, your body is not in the business of absorbing whole proteins. Trypsin is one of the enzymes used to reduce peptides (protein fragments) into even smaller blocks (often down to amino acids). So yeah, whether or not that protein is denatured before your duodenum, it sure as hell will be afterwards. At least, so one hopes.