[Article] New Software for the Identification and Characterization of Peptides Generated during Fontina Cheese Ripening Using Mass Spectrometry Data

The microbiological profile in raw milk cheese is typically characterized by a multitude of microbial groups; during cheese ripening a wide range of enzymes interact, hydrolysing caseins into peptides and free amino acids. Although a number of microbial enzymes are common to many cheese varieties, the final peptide composition of a cheese reflects its characteristic ripening process. The peptide profile composition differs according to different stages of ageing, type of manufacturing, and territory, resulting in the flavour and texture characteristic of the particular variety. The peptide profile may cover thousands of peptides derived from the four original casein molecules of different genetic and chemical variants and other, recently discovered, of non-proteolytic origin but synthesised de novo in cheese by enzymatic activities. An effective way of acquiring more information on the proteolytic process in cheese is to identify the peptides produced throughout ripening. Some proteolytic peptides have been identified in exploratory studies mainly using amino acid sequencing and mass spectrometry, but little information is available on the peptide profile of Fontina cheese, an Italian semi-hard and semi-cooked cheese. Nowadays various software, available online, allow users to identify proteins but all of them are focused on human or human model proteins data sets. Furthermore the peptides data-base used for molecular weight matching are generated by in-silico digestion with only few proteolytic enzymes. The aim of this work was to design and implement a new bioinformatics software which is able to identify the protein peptides from the peaks arising from in-source or MS/MS fragmentation.