title: Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks.
abstract: Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.
authors.affiliation: Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; email: fwhite@mit.edu.
authors.forename: Forest M
authors.initials: FM
authors.lastname: White
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98105; email: ayadlin@uw.edu.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Wolf-Yadlin
mesh_terms: D000818:Animals; D006801:Humans; D010766:Phosphorylation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D011506:Proteins
keywords: PhosphoFlow cytometry; phosphoproteomics; phosphorylation; phosphorylation motif; signaling networks; targeted approaches