Milk samples with twelve combinations of κ- and β-casein (CN) and β-lactoglobulin (β-Lg) variants were obtained to investigate the effect of protein variant on the mechanism/s of age gelation in ultra-high temperature (UHT) skim milk. Only milk groups with κ-CN/β-CN/β-Lg combinations AB/A1A2/AB and AB/A2A2/AB suffered from the expected age gelation over nine months storage, although this could not be attributed to the milk protein genetic variants. Top-down proteomics revealed three general trends across the twelve milk groups: (1) the abundance of intact native proteins decreases over storage time; (2) lactosylated proteoforms appear immediately post-UHT treatment; and (3) protein degradation products accumulate over storage time. Of the 151 identified degradation products, 106 (70.2%) arose from β-CN, 33 (21.9%) from αs1
-CN, 4 (2.7%) from β-Lg, 4 (2.7%) from α-La, 3 (2%) from κ-CN and 1 (0.7%) from αs2
-CN. There was a positive correlation between milk viscosity and 47 short peptides and four intact proteoforms, while 20 longer polypeptides and 21 intact proteoforms were negatively correlated. Age gelation was associated with specific patterns of proteolytic degradation and also with the absence of the families Bacillaceae
, present in all the non-gelling milk groups pre-UHT.
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