Background: The prognosis of gastric cancer remains poor despite the recent improvements in therapies. The aim of this study was to develop a novel strategy to discover gastric cancer-specific peptides in sera. Methods: Here, Fe₃O₄@mSiO₂ microspheres were prepared to separate and enrich serum peptides in patients with gastric cancer. Stable isotope labeling coupled with LC-MALDI then quantified those differentially expressed peptides. In contrast with the commonly used strategy, this novel strategy was more efficient and sensitive, which also enabled the accurate identification and quantification of serum peptides. Results: Based on this strategy, the results showed that serum CK18, apoE, C3 precursor, Clusterin, C4a, HMW-kininogen, apoA-4 and ghrelin peptides were differentially expressed significantly in patients, especially when there had been no available information concerning the serum level of active ghrelin in predicting gastric cancer. In addition, our data demonstrated that serum active ghrelin expression was closely correlated with shorter survival in patients which would show biological activity for promotion of lymph node metastasis. Conclusions: Active ghrelin might be a novel circulating biomarker in the prognosis of gastric cancer.