title: Computational analysis of phosphoproteomics: progresses and perspectives.
abstract: Phosphorylation is one of the most essential post-translational modifications (PTMs) of proteins, regulates a variety of cellular signaling pathways, and at least partially determines the biological diversity. Recent progresses in phosphoproteomics have identified more than 100,000 phosphorylation sites, while this number will easily exceed one million in the next decade. In this regard, how to extract useful information from flood of phosphoproteomics data has emerged as a great challenge. In this review, we summarized the leading edges on computational analysis of phosphoproteomics, including discovery of phosphorylation motifs from phosphoproteomics data, systematic modeling of phosphorylation network, analysis of genetic variation that influences phosphorylation, and phosphorylation evolution. Based on existed knowledge, we also raised several perspectives for further studies. We believe that integration of experimental and computational analyses will propel the phosphoproteomics research into a new phase.
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University (SYSU), Guangzhou, Guangdong 510275, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ren
authors.forename: Xinjiao
authors.initials: X
authors.lastname: Gao
authors.forename: Zexian
authors.initials: Z
authors.lastname: Liu
authors.forename: Jun
authors.initials: J
authors.lastname: Cao
authors.forename: Qian
authors.initials: Q
authors.lastname: Ma
authors.forename: Yu
authors.initials: Y
authors.lastname: Xue
mesh_terms: D020816:Amino Acid Motifs; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D014644:Genetic Variation; D008954:Models, Biological; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D040901:Proteomics
chemical_list: D010750:Phosphoproteins