To identify proteins contributing to meat quality, a comparative shotgun proteomic profiling of Berkshire loin was conducted in high pH group (HpHG) and low pH group (LpHG) based on 24 hour post-mortem pH (pH24hr). Triplicate liquid chromatography-tandem mass spectrometry analysis revealed a total of 208 and 204 proteins in the HpHG and LpHG, respectively. Noticeably, the dominant expressions of Aco2, IGC, LDH-B, and PREP were identified in the LpHG by shotgun proteomic analysis and confirmed by RT-PCR, indicating biomarkers suitable for determining meat quality. Moreover, PREP promoter was discovered to be methylated differentially between the HpHG and LpHG, suggesting the epigenetic regulation of gene expression responsive to the pH24hr.