ABSTRACT: Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.
xiaomei li 
