title: Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity.
abstract: BACKGROUND
  Protein phosphorylation is the most common post-translational modification (PTM) regulating major cellular processes through highly dynamic and complex signaling pathways. Large-scale comparative phosphoproteomic studies have frequently been done on whole cells or organs by conventional bottom-up mass spectrometry approaches, i.e at the phosphopeptide level. Using this approach, there is no way to know from where the phosphopeptide signal originated. Also, as a consequence of the scale of these studies, important information on the localization of phosphorylation sites in subcellular compartments (SCs) is not surveyed.
  
  
  RESULTS
  Here, we present a first account of the emerging field of subcellular phosphoproteomics where a support vector machine (SVM) approach was combined with a novel algorithm of discrete wavelet transform (DWT) to facilitate the identification of compartment-specific phosphorylation sites and to unravel the intricate regulation of protein phosphorylation. Our data reveal that the subcellular phosphorylation distribution is compartment type dependent and that the phosphorylation displays site-specific sequence motifs that diverge between SCs.
  
  
  METHODS
  The method and database both are available as a web server at: http://bioinfo.ncu.edu.cn/SubPhos.aspx.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China.
authors.forename: Shao-Ping
authors.initials: SP
authors.lastname: Shi
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China.
authors.forename: Sheng-Bao
authors.initials: SB
authors.lastname: Suo
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China.
authors.forename: Hao-Dong
authors.initials: HD
authors.lastname: Xu
authors.affiliation: Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China Department of Chemistry, Nanchang University, Nanchang 330031, Department of Mathematics, Nanchang University, Nanchang 330031 and Department of Materials and Chemical Engineering, Pingxiang College, Pingxiang 337055, P.R. China.
authors.forename: Jian-Ding
authors.initials: JD
authors.lastname: Qiu
mesh_terms: D000465:Algorithms; D006801:Humans; D013058:Mass Spectrometry; D010748:Phosphopeptides / Q000032:analysis*; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D013347:Subcellular Fractions; D060388:Support Vector Machine
chemical_list: D010748:Phosphopeptides; D020543:Proteome