Literature DB >> 26960075

The current state of the art of quantitative phosphoproteomics and its applications to diabetes research.

Chi Yuet X'avia Chan1, Marina A Gritsenko1, Richard D Smith1, Wei-Jun Qian1.   

Abstract

Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.

Entities:  

Keywords:  LC-MS/MS; Phosphoproteomics; diabetes; phosphopeptide enrichment; phosphorylation; quantification; targeted proteomics

Mesh：

Substances：

Year:  2016        PMID： 26960075      PMCID： PMC4939282          DOI： 10.1586/14789450.2016.1164604

Source DB:  PubMed          Journal:  Expert Rev Proteomics        ISSN： 1478-9450            Impact factor:   3.940


  138 in total

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Authors:  John Rush; Albrecht Moritz; Kimberly A Lee; Ailan Guo; Valerie L Goss; Erik J Spek; Hui Zhang; Xiang-Ming Zha; Roberto D Polakiewicz; Michael J Comb
Journal:  Nat Biotechnol       Date:  2004-12-12       Impact factor: 54.908

2.  SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides.

Authors:  Tine E Thingholm; Ole N Jensen; Phillip J Robinson; Martin R Larsen
Journal:  Mol Cell Proteomics       Date:  2007-11-26       Impact factor: 5.911

3.  Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.

Authors:  Sharon Gauci; Andreas O Helbig; Monique Slijper; Jeroen Krijgsveld; Albert J R Heck; Shabaz Mohammed
Journal:  Anal Chem       Date:  2009-06-01       Impact factor: 6.986

4.  In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling.

Authors:  Paul J Boersema; Leong Yan Foong; Vanessa M Y Ding; Simone Lemeer; Bas van Breukelen; Robin Philp; Jos Boekhorst; Berend Snel; Jeroen den Hertog; Andre B H Choo; Albert J R Heck
Journal:  Mol Cell Proteomics       Date:  2009-09-21       Impact factor: 5.911

5.  Antibody suspension bead arrays.

Authors:  Jochen M Schwenk; Peter Nilsson
Journal:  Methods Mol Biol       Date:  2011

Review 6.  Understanding the Cellular and Molecular Mechanisms of Physical Activity-Induced Health Benefits.

Authors:  P Darrell Neufer; Marcas M Bamman; Deborah M Muoio; Claude Bouchard; Dan M Cooper; Bret H Goodpaster; Frank W Booth; Wendy M Kohrt; Robert E Gerszten; Mark P Mattson; Russell T Hepple; William E Kraus; Michael B Reid; Sue C Bodine; John M Jakicic; Jerome L Fleg; John P Williams; Lyndon Joseph; Mary Evans; Padma Maruvada; Mary Rodgers; Mary Roary; Amanda T Boyce; Jonelle K Drugan; James I Koenig; Richard H Ingraham; Danuta Krotoski; Mary Garcia-Cazarin; Joan A McGowan; Maren R Laughlin
Journal:  Cell Metab       Date:  2015-06-11       Impact factor: 27.287

7.  In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis.

Authors:  Sara Zanivan; Alexander Meves; Kristina Behrendt; Erwin M Schoof; Lisa J Neilson; Jürgen Cox; Hao R Tang; Gabriela Kalna; Janine H van Ree; Jan M van Deursen; Carol S Trempus; Laura M Machesky; Rune Linding; Sara A Wickström; Reinhard Fässler; Matthias Mann
Journal:  Cell Rep       Date:  2013-01-31       Impact factor: 9.423

8.  An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells.

Authors:  Tyler H Heibeck; Shi-Jian Ding; Lee K Opresko; Rui Zhao; Athena A Schepmoes; Feng Yang; Aleksey V Tolmachev; Matthew E Monroe; David G Camp; Richard D Smith; H Steven Wiley; Wei-Jun Qian
Journal:  J Proteome Res       Date:  2009-08       Impact factor: 4.466

9.  A phase II clinical trial of sorafenib in androgen-independent prostate cancer.

Authors:  William L Dahut; Charity Scripture; Edwin Posadas; Lokesh Jain; James L Gulley; Philip M Arlen; John J Wright; Yunkai Yu; Liang Cao; Seth M Steinberg; Jeanny B Aragon-Ching; Jürgen Venitz; Elizabeth Jones; Clara C Chen; William D Figg
Journal:  Clin Cancer Res       Date:  2008-01-01       Impact factor: 12.531

10.  Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy.

Authors:  Jinyan Du; Paula Bernasconi; Karl R Clauser; D R Mani; Stephen P Finn; Rameen Beroukhim; Melissa Burns; Bina Julian; Xiao P Peng; Haley Hieronymus; Rebecca L Maglathlin; Timothy A Lewis; Linda M Liau; Phioanh Nghiemphu; Ingo K Mellinghoff; David N Louis; Massimo Loda; Steven A Carr; Andrew L Kung; Todd R Golub
Journal:  Nat Biotechnol       Date:  2008-12-21       Impact factor: 54.908
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  7 in total

Review 1.  Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials.

Authors:  Tong Zhang; Matthew J Gaffrey; Brian D Thrall; Wei-Jun Qian
Journal:  Anal Bioanal Chem       Date:  2018-06-08       Impact factor: 4.142

2.  Impact of Phosphorylation on the Mass Spectrometry Quantification of Intact Phosphoproteins.

Authors:  Zhijie Wu; Timothy N Tiambeng; Wenxuan Cai; Bifan Chen; Ziqing Lin; Zachery R Gregorich; Ying Ge
Journal:  Anal Chem       Date:  2018-03-26       Impact factor: 6.986

Review 3.  Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines.

Authors:  Jicheng Duan; Matthew J Gaffrey; Wei-Jun Qian
Journal:  Mol Biosyst       Date:  2017-05-02

4.  Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway.

Authors:  Lian Yi; Tujin Shi; Marina A Gritsenko; Chi-Yuet X'avia Chan; Thomas L Fillmore; Becky M Hess; Adam C Swensen; Tao Liu; Richard D Smith; H Steven Wiley; Wei-Jun Qian
Journal:  Anal Chem       Date:  2018-04-03       Impact factor: 6.986

Review 5.  Advances in microscale separations towards nanoproteomics applications.

Authors:  Lian Yi; Paul D Piehowski; Tujin Shi; Richard D Smith; Wei-Jun Qian
Journal:  J Chromatogr A       Date:  2017-07-21       Impact factor: 4.759

Review 6.  Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation.

Authors:  T E Thingholm; L Rönnstrand; P A Rosenberg
Journal:  Cell Mol Life Sci       Date:  2020-02-19       Impact factor: 9.261

7.  Fractionation of Enriched Phosphopeptides Using pH/Acetonitrile-Gradient-Reversed-Phase Microcolumn Separation in Combination with LC-MS/MS Analysis.

Authors:  Martin Ondrej; Pavel Rehulka; Helena Rehulkova; Rudolf Kupcik; Ales Tichy
Journal:  Int J Mol Sci       Date:  2020-06-01       Impact factor: 5.923
  7 in total

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