From the prediction models-based analysis, two panels proved particularly effective: ARG1, CA2, HPT, MAN2A1, and LBP (mAUROC: 83.9%; 73.9–93.9% (95% CI)) for differentiating patients with cancer or precancerous lesions from healthy individuals or patients with gastritis; and ARG1, CA2, F13A1 and S100A12 (mAUROC: 85.3%; 72.8–97.8% (95% CI)) for differentiating GC from non-cancer patients. Here, MRS2 is linked to gastritis.