Identification of biologically active peptides in food matrices is a challenging task in food technology. In the present study, we propose a strategy for the rapid identification of peptides in complex food fractions and targeting of potentially bioactive peptides according to previous studies of activity-structure relationship. A large number of peptides included in the Mr 3000 permeate of a fermented product and its hydrolysate (obtained by simulated gastrointestinal digestion) could be easily identified using HPLC coupled on line to an ion trap mass spectrometer. Three of the identified sequences have previously been described as angiotensin-converting enzyme (ACE) inhibitors. The sequence of some peptides allowed us to anticipate the presence of ACE-inhibitory activity and several peptides were selected to initiate studies on antihypertensive, antioxidant and cytomodulatory activity.