Invited review: Proteomics of milk and bacteria used in fermented dairy products: From qualitative to quantitative advances

Proteomics is a powerful tool that can simultaneously analyze several hundred proteins in complex mixtures, either through the use of high-resolution 2-dimensional gel electrophoresis or by mono- and multi-dimensional liquid chromatography coupled with mass spectrometry. Since the last review in 2005, proteomics has mainly been applied to describe minor proteins in the bovine milk fat globule membrane and soluble proteins in human colostrum. At least 130 new minor proteins have been identified. These proteins play roles in cell signaling, host defense, and transport as suggested by sequence homology. Proteomic approaches have also been applied to milk of other species such as donkey, horse, and marsupial. Peptides produced in food matrices that can exhibit functional or bioactive properties have been identified as have the proteases leading to their release in situ. However, the most spectacular proteomic development has been in the field of bacteria used in dairy products. Proteomics has resulted in the establishment of reference maps to detect strain-to-strain variations and to elucidate the mechanisms of in vitro and in vivo adaptation to environmental conditions. Proteomic analysis of bacteria entrapped in cheese has been achieved and revealed which predominant metabolic pathways are active depending on the strain. Proteomic approaches are often evoked as time-consuming procedures that provide a list of identified proteins without efficient quantification of each one. New quantitative proteomic methods have emerged and the most promising ones and their application to dairy products and bacteria will be presented.