Proteomics-Led Multi-Omics Analysis Characterizes Candidate Molecular Features Accompanying Higher IMP Content in the Longissimus dorsi Muscle of New Jilin Black Pigs

Inosine 5′-monophosphate (IMP) is an important umami-associated nucleotide in meat, yet whether New Jilin Black (NJ) and Duroc × Landrace × Yorkshire (DLY) pigs differ in longissimus dorsi muscle IMP content and which molecular features accompany any such difference remain unclear. Longissimus dorsi muscles from six intact male pigs per breed, selected at similar body weight but not matched for age, were analyzed using targeted IMP quantification and a proteomics-led multi-omics strategy. IMP quantification and untargeted metabolomics used six pigs per breed, whereas proteomic and transcriptomic analyses used four randomly selected pigs per breed. IMP content was higher in NJ than in DLY (1965.0 ± 134.0 vs. 1407.7 ± 115.1 mg/kg; p < 0.0001). Two proteins met proteome-wide FDR and fold-change criteria, whereas RPIA, GART, NT5C1A, and NUDT16 were retained as exploratory purine-related candidates. Metabolomics identified 279 FDR- and fold-change-supported differential features, including features annotated as hypoxanthine, xanthosine, and guanine with higher relative abundance and a feature annotated as adenylosuccinic acid with lower relative abundance in NJ. Corresponding transcripts showed the same NJ/DLY direction but were not significant after multiple-testing correction. These findings provide a phenotype-oriented, hypothesis-generating molecular context accompanying the higher measured IMP content in NJ and require independent targeted, functional, and sensory validation.