Investigating changes of proteome in the bovine milk serum after retort processing using proteomics techniques

BoMiProt 2.0: An update of the bovine milk protein database

Milk is a biofluid with various functions, containing carbohydrates, lipids, proteins, vitamins, and minerals. Owing to its importance and availability of vast proteomics information, our research group designed a database for bovine milk proteins (N = 3159) containing the primary and secondary information called BoMiProt. Due to the gaining interest and intensively published literature in the last three years, BoMiProt has been upgraded with newer identified proteins (N = 7459) from peer-reviewed journals, significantly expanding the database from different milk fractions (e.g., whey, fat globule membranes, and exosomes). Additionally, class, architecture, topology, and homology, structural classification of proteins, known and predicted disorder, predicted transmembrane helices, and structures have been included. Each protein entry in the database is thoroughly cross-referenced, including 1392 BoMiProt defined proteins provided with secondary information, such as protein function, biochemical properties, post-translational modifications, significance in milk, domains, fold, AlphaFold predicted models and crystal structures. The proteome data in the database can be retrieved using several search parameters using protein name, accession IDs, and FASTA sequence. Overall, BoMiProt represents an extensive compilation of newer proteins, including structural, functional, and hierarchical information, to help researchers better understand mammary gland pathophysiology, including their potential application in improving the nutritional quality of dairy products.