This project contains raw LC-MS/MS data and processed pGlyco3 output files from a TMT6-labeled serum N-glycoproteomic study of human gastric cancer samples. TMT channels 126, 127 and 128 correspond to the non-metastasis group, while TMT channels 129, 130 and 131 correspond to the metastasis group. Glycopeptide identification and quantification were performed using pGlyco3.