Temporal perturbation of tyrosine phosphoproteome dynamics reveals the system-wide regulatory networks

Mol Cell Proteomics. 2009 Feb;8(2):226-31. doi: 10.1074/mcp.M800186-MCP200. Epub 2008 Sep 24.


Signal transduction systems are known to widely regulate complex biological events such as cell proliferation and differentiation. Because phosphotyrosine-dependent networks play a key role in transmitting signals, a comprehensive and fine description of their dynamic behavior can lead us to systematically analyze the regulatory mechanisms that result in each biological effect. Here we established a mass spectrometry-based framework for analyzing tyrosine phosphoproteome dynamics through temporal network perturbation. A highly time-resolved description of the epidermal growth factor-dependent signaling pathways in human A431 cells revealed a global view of their multiphase network activation, comprising a spike signal transmission within 1 min of ligand stimulation followed by the prolonged activation of multiple Src-related molecules. Temporal perturbation of Src family kinases with the corresponding inhibitor PP2 in the prolonged activation phase led to the down-regulation of the molecules related to cell adhesion and receptor degradation, whereas the canonical cascades as well as the epidermal growth factor receptor relatively maintained their activities. Our methodology provides a system-wide view of the regulatory network clusters involved in signal transduction that is essential to refine the literature-based network structures for a systems biology analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Epidermal Growth Factor / pharmacology
  • Gene Regulatory Networks* / drug effects
  • Humans
  • Phosphorylation / drug effects
  • Phosphotyrosine / metabolism*
  • Proteome / metabolism*
  • Pyrimidines / pharmacology
  • Time Factors
  • src-Family Kinases / antagonists & inhibitors


  • AG 1879
  • Proteome
  • Pyrimidines
  • Phosphotyrosine
  • Epidermal Growth Factor
  • src-Family Kinases