Genetic variation of milk proteins produces milks with vastly different functionalities. For example, it is known that milk composed of A κ-casein and A2 β-casein is less likely to form a rennet gel, the first step in the cheese making process. In this experiment twelve milk groups were selected with specific κ- and β-casein and β-lactoglobulin variants to determine if a particular combination of milk proteins provides a more shelf-stable UHT skim milk. Another aim was to investigate the mechanism/s of age gelation on milks controlled for protein variation. Out of the twelve milk groups, group 9 (AB κ-CN, A1A2 β-CN and AB β-Lg) and group 11 (AB κ-CN, A2A2 β-CN and AB β-Lg) suffered from age gelation over the storage time of nine months, although this was not attributed to the milk protein genetic variants. Top-down mass spectrometry analyses identified 209 protein compounds and numerous post-translational modifications, including 58 intact proteoforms and 151 degradation products. UHT treatment induced lactosylation of the most abundant proteins. All twelve groups of milk suffered from proteolytic degradation during storage. Overall 47 peptides were positively associated with high viscosity; 34 (72%) resulted from β-casein proteolysis, and 20 of these (59%) had cleavage sites previously identified from the extracellular heat stable protease AprX from Pseudomonas. Microbial population analysis of the raw milks prior to UHT treatment showed several bacterial taxa lacking in the two groups that suffered from age gelation. Age gelation in these milks could have been initiated by specific proteolytic degradation and a lower microbial diversity may have also contributed to this mechanism.