The alteration extents in global proteome, site-specific glycosylation and glycosylation occupancy in different HCC samples were systematically compared, and altered site-specific N-glycans that commonly or uniquely identified from HCC tumors with low and high AFP were analyzed based on their glycan features and involved Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. This evidence concerns the gene AFP and hepatocellular carcinoma.