The results showed that LAT2/SPRY2 (OR: 0.9992, 95% CI: 0.9986–0.9999; p = 0.018), FAP/THBS4 (OR: 0.9997, 95% CI: 0.9994–0.9999; p = 0.012), ICA1/IRAK1 (OR: 1.0002, 95% CI: 1–1.0004; p = 0.033), ERBIN/LAT2 (OR: 1.0006, 95% CI: 1.0002–1.0009); and ITGB1BP2/LAT2 (OR: 1.0004, 95% CI: 1.0001–1.0007; p < 0.005), a total of 51 protein pairs, were linked to an increased risk of HCC. Here, SPRY2 is linked to hepatocellular carcinoma.