Literature DB >> 18619541

Quantitative phosphoproteomic analysis of signaling network dynamics.

Forest M White1.   

Abstract

Protein phosphorylation mediated cellular signaling is a highly regulated, dynamic process that controls many aspects of cellular biology. Over the past few years many methods have been developed to quantify temporal dynamics of protein phosphorylation, including mass spectrometry, which can be applied in both an unbiased, discovery mode and in a targeted mode to monitor specific phosphorylation sites. Other methods, such as kinase activity assays and antibody microarrays, have been applied to quantify central nodes in the signaling network, yielding intriguing biological insights. This review provides a concise overview of the latest advances in the quantitative analysis of signaling dynamics including a brief commentary on the future of the field.

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Year:  2008        PMID: 18619541      PMCID: PMC2567239          DOI: 10.1016/j.copbio.2008.06.006

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  26 in total

Review 1.  Oncogenic kinase signalling.

Authors:  P Blume-Jensen; T Hunter
Journal:  Nature       Date:  2001-05-17       Impact factor: 49.962

2.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry.

Authors:  John E P Syka; Joshua J Coon; Melanie J Schroeder; Jeffrey Shabanowitz; Donald F Hunt
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-21       Impact factor: 11.205

3.  Causal protein-signaling networks derived from multiparameter single-cell data.

Authors:  Karen Sachs; Omar Perez; Dana Pe'er; Douglas A Lauffenburger; Garry P Nolan
Journal:  Science       Date:  2005-04-22       Impact factor: 47.728

4.  A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

Authors:  Kevin A Janes; John G Albeck; Suzanne Gaudet; Peter K Sorger; Douglas A Lauffenburger; Michael B Yaffe
Journal:  Science       Date:  2005-12-09       Impact factor: 47.728

5.  Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations.

Authors:  Joshua E Elias; Wilhelm Haas; Brendan K Faherty; Steven P Gygi
Journal:  Nat Methods       Date:  2005-09       Impact factor: 28.547

Review 6.  A biological approach to computational models of proteomic networks.

Authors:  Kevin A Janes; Douglas A Lauffenburger
Journal:  Curr Opin Chem Biol       Date:  2006-01-06       Impact factor: 8.822

7.  Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

Authors:  James J Pesavento; Courtney R Bullock; Richard D LeDuc; Craig A Mizzen; Neil L Kelleher
Journal:  J Biol Chem       Date:  2008-04-01       Impact factor: 5.157

8.  Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules.

Authors:  Yi Zhang; Alejandro Wolf-Yadlin; Phillip L Ross; Darryl J Pappin; John Rush; Douglas A Lauffenburger; Forest M White
Journal:  Mol Cell Proteomics       Date:  2005-06-11       Impact factor: 5.911

9.  Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics.

Authors:  Blagoy Blagoev; Shao-En Ong; Irina Kratchmarova; Matthias Mann
Journal:  Nat Biotechnol       Date:  2004-08-15       Impact factor: 54.908

10.  Single cell profiling of potentiated phospho-protein networks in cancer cells.

Authors:  Jonathan M Irish; Randi Hovland; Peter O Krutzik; Omar D Perez; Øystein Bruserud; Bjørn T Gjertsen; Garry P Nolan
Journal:  Cell       Date:  2004-07-23       Impact factor: 41.582

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  26 in total

1.  Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations.

Authors:  Michael Dworkin; Sayak Mukherjee; Ciriyam Jayaprakash; Jayajit Das
Journal:  J R Soc Interface       Date:  2012-02-29       Impact factor: 4.118

Review 2.  Proteomics: a pragmatic perspective.

Authors:  Parag Mallick; Bernhard Kuster
Journal:  Nat Biotechnol       Date:  2010-07-09       Impact factor: 54.908

3.  LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

Authors:  Damian Fermin; Scott J Walmsley; Anne-Claude Gingras; Hyungwon Choi; Alexey I Nesvizhskii
Journal:  Mol Cell Proteomics       Date:  2013-08-05       Impact factor: 5.911

Review 4.  Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Authors:  Peter Csermely; Tamás Korcsmáros; Huba J M Kiss; Gábor London; Ruth Nussinov
Journal:  Pharmacol Ther       Date:  2013-02-04       Impact factor: 12.310

Review 5.  Studying and modelling dynamic biological processes using time-series gene expression data.

Authors:  Ziv Bar-Joseph; Anthony Gitter; Itamar Simon
Journal:  Nat Rev Genet       Date:  2012-07-18       Impact factor: 53.242

6.  Determining in vivo phosphorylation sites using mass spectrometry.

Authors:  Susanne B Breitkopf; John M Asara
Journal:  Curr Protoc Mol Biol       Date:  2012-04

Review 7.  Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling.

Authors:  Bin Fang; Eric B Haura; Keiran S Smalley; Steven A Eschrich; John M Koomen
Journal:  Biochem Pharmacol       Date:  2010-03-31       Impact factor: 5.858

8.  Fast rebinding increases dwell time of Src homology 2 (SH2)-containing proteins near the plasma membrane.

Authors:  Dongmyung Oh; Mari Ogiue-Ikeda; Joshua A Jadwin; Kazuya Machida; Bruce J Mayer; Ji Yu
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-10       Impact factor: 11.205

9.  Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways.

Authors:  Cemal Erdem; Alison M Nagle; Angelo J Casa; Beate C Litzenburger; Yu-Fen Wang; D Lansing Taylor; Adrian V Lee; Timothy R Lezon
Journal:  Mol Cell Proteomics       Date:  2016-06-30       Impact factor: 5.911

10.  Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics.

Authors:  Maximiliane Hilger; Tiziana Bonaldi; Florian Gnad; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2009-05-09       Impact factor: 5.911

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