Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

M. Hjerrild, A. Stensballe, T.E. Rasmussen, C.B. Kofoed, Nikolaj Blom, Thomas Sicheritz-Pontén, M.R. Larsen, Søren Brunak, O.N. Jensen, S. Gammeltoft

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    Abstract

    Protein phosphorylation plays a key role in cell regulation and identification of phosphorylation sites is important for understanding their functional significance. Here, we present an artificial neural network algorithm: NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/) that predicts protein kinase A (PKA) phosphorylation sites. The neural network was trained with a positive set of 258 experimentally verified PKA phosphorylation sites. The predictions by NetPhosK were! validated using four novel PKA substrates: Necdin, RFX5, En-2, and Wee 1. The four proteins were phosphorylated by PKA in vitro and 13 PKA phosphorylation sites were identified by mass spectrometry. NetPhosK was 100% sensitive and 41% specific in predicting PKA sites in the four proteins. These results demonstrate the potential of using integrated computational and experimental methods for detailed investigations of the phosphoproteome.
    Original languageEnglish
    JournalJournal of Proteome Research
    Volume3
    Pages (from-to)426-433
    Publication statusPublished - 2004

    Cite this

    Hjerrild, M., Stensballe, A., Rasmussen, T. E., Kofoed, C. B., Blom, N., Sicheritz-Pontén, T., Larsen, M. R., Brunak, S., Jensen, O. N., & Gammeltoft, S. (2004). Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. Journal of Proteome Research, 3, 426-433.