We applied capillary electrophoresis, liquid chromatography coupled with tandem mass-spectrometry (MS/MS), and ultra-performance liquid chromatography to determine the composition of water-insoluble and water-soluble proteinaceous fractions of the cheese and to study in detail the degradation of caseins during 8 mo of ripening of Estonian high-temperature cooked hard cheese Old Saare. The application of high-resolution and high-accuracy MS/MS enabled identification of more than 3,000 small peptides, representing a fairly full casein peptidome containing peptides of 4 to 25 AA in length: 1,049 from β-casein (CN), 944 from αS1-CN, 813 from αS2-CN, and 234 from κ-CN. The majority of β-CN- and αS1-CN-derived peptides originated from the N-terminal parts of the molecule, f6-93 and f1-124, respectively; peptides from αS2-CN arose predominantly from the C-terminal end f100-162. At the beginning of ripening, we found a relatively high amount of peptides originating from the glycomacropeptide part of κ-CN, whereas peptides from para-κ-CN prevailed during the later stages of ripening of the cheese. The cleavage patterns of β-CN, αS2-CN, as well as αS1-CN, showed that primary proteolysis was started mainly by plasmin, although a low proteolytic activity of chymosin was also evident. Based on the analysis of cleavage sites, we observed a significant participation of proteolytic enzymes, including amino- and carboxypeptidases, of both mesophilic and thermophilic starter bacteria in further hydrolysis of oligopeptides during the ripening. Several new phosphopeptides were detected in the result of MS/MS data analysis. The profiles of the estimated concentrations of phosphopeptides revealed that those originating from β-CN and αS1-CN accumulated during cheese maturation. In contrast, we did not notice any generation of phosphopeptides from the highly phosphorylated part of αS2-CN, f25-80, presumably due to the inaccessibility of this region to the action of plasmin and chymosin. The analysis of cleavage sites and the combination of principal component and clustering analyses provided a characterization of the complex dynamics of formation and degradation of peptides during cheese maturation. We made an attempt to obtain a comprehensive picture of proteolysis during Old Saare cheese ripening on the basis of the detailed peptidomic data, including also the less abundant peptides determined by MS/MS, and complemented by the data on intact caseins and free AA and reported the results in the paper.

The application of reverse osmosis (RO) for preconcentration of milk (RO-milk) on farms can decrease the overall transportation costs of milk, increase the capacity of cheese production, and may be highly attractive from the cheese manufacturer’s viewpoint. In this study, an attempt was made to produce a hard cheese from RO-milk with a concentration factor of 1.9 (RO-cheese). Proteolysis, volatile profiles, and sensory properties were evaluated throughout six months of RO-cheese ripening. Moderate primary proteolysis took place during RO-cheese ripening: about 70% of α_s1-casein and 45% of β-casein were hydrolyzed by the end of cheese maturation. The total content of free amino acids (FAA) increased from 4.3 to 149.9 mmol kg⁻¹, with Lys, Pro, Glu, Leu, and γ-aminobutyric acid dominating in ripened cheese. In total, 42 volatile compounds were identified at different stages of maturation of RO-cheese; these compounds have previously been found in traditional Gouda-type and hard-type cheeses of prolonged maturation. Fresh RO-cheese was characterized by a milky and buttery flavor, whereas sweetness, saltiness, and umami flavor increased during ripening. Current results prove the feasibility of RO-milk for the production of hard cheese with acceptable sensory characteristics and may encourage further research and implementation of RO technology in cheese manufacture.

Hypoallergenic formulas containing hydrolyzed protein are intended for use by infants to prevent cow’s milk protein allergy. The degree of hydrolysis of epitopic areas determines the residual allergenicity of whey protein hydrolysates (WPHs). However, only amino-acid-based infant formulas (IFs) are considered entirely nonallergenic. The aim of this study was to investigate four commercially available WPHs with different degree of hydrolysis (H1–H4) for potential allergenicity, by applying LC-HRMS analysis of peptides, and using in silico tools to search for the immunoglobulin (IgE)-binding allergenic epitopes from the Immune Epitope Database. Additionally, the molecular weight distribution of proteins and peptides in the WPHs was measured by SE-UPLC. Based on the peptide coverage and peptide-length distribution profiles, the WPHs showed different extents of hydrolysis: extensively (H1 and H2), partially (H3), and slightly hydrolyzed (H4). Altogether, numerous peptides related to 46 specific IgE-binding epitopes from β-lactoglobulin and α-lactalbumin were found in all the WPHs, regardless of their extent of hydrolysis. Sequence-based identification of the specific peptide composition, with an application of in silico tools, is a reliable approach for discovering the potential allergenicity of protein hydrolysates for IFs.

Until now, cheese peptidomics approaches have been criticised for their lower throughput. Namely, analytical gradients that are most commonly used for mass spectrometric detection are usually over 60 or even 120 min. We developed a cheese peptide mapping method using nano ultra-high-performance chromatography data-independent acquisition high-resolution mass spectrometry (nanoUHPLC-DIA-HRMS) with a chromatographic gradient of 40 min. The 40 min gradient did not show any sign of compromise in milk protein coverage compared to 60 and 120 min methods, providing the next step towards achieving higher-throughput analysis. Top 150 most abundant peptides passing selection criteria across all samples were cross-referenced with work from other publications and a good correlation between the results was found. To achieve even faster sample turnaround enhanced DIA methods should be considered for future peptidomics applications.