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Proteomics - Resources

Publications - last updated February, 2016

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Chen Z, Lessey E, Berginski ME, Cao L, Li J, Trepat X, Itano M, Gomez SM, Kapustina M, Huang C, Burridge K, Truskey G, Jacobson K. Gleevec, an abl family inhibitor, produces a profound change in cell shape and migration. PLoS ONE 2013; 8:e52233 Full Text | CMC Update Article.

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  • Banno A, Goult BT, Lee H, Bate N, Critchley DR, Ginsberg MH. Subcellular localization of talin is regulated by inter-domain interactions. J Biol Chem 2012; PubMed | CMC Update Article.
  • Bate N, Gingras AR, Bachir A, Horwitz R, Ye F, Patel B, Goult BT, Critchley DR. Talin contains a C-terminal calpain2 cleavage site important in focal adhesion dynamics. PLoS ONE 2012; 7:e34461 Full Text | CMC Update Article.
  • Grigera PR, Ma L, Borgman CA, Pinto AF, Sherman NE, Parsons JT, Fox JW. Mass spectrometric analysis identifies a cortactin-RCC2/TD60 interaction in mitotic cells. J Proteomics 2012; PubMed.
  • Kelber JA, Reno T, Kaushal S, Metildi C, Wright T, Stoletov K, Weems JM, Park FD, Mose E, Wang Y, Hoffman RM, Lowy AM, Bouvet M, Klemke RL. KRas induces a Src/PEAK1/ErbB2 kinase amplification loop that drives metastatic growth and therapy resistance in pancreatic cancer. Cancer Res. 2012; 72:2554-64 Full Text | CMC Update Article.
  • Wang Y, Klemke RL. Proteomics method for identification of pseudopodium phosphotyrosine proteins. Methods Mol. Biol. 2012; 757:349-65 PubMed | CMC Update Article.

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  • Kim J, Sherman NE, Fox JW, Ginsberg MH. Phosphorylation sites in the cerebral cavernous malformations complex. J. Cell. Sci. 2011; 124:3929-32 Full Text | CMC Update Article.
  • Liu JJ, Stockton RA, Gingras AR, Ablooglu AJ, Han J, Bobkov AA, Ginsberg MH. A mechanism of Rap1-induced stabilization of endothelial cell--cell junctions. Mol. Biol. Cell 2011; 22:2509-19 Full Text.
  • Sundd P, Gutierrez E, Petrich BG, Ginsberg MH, Groisman A, Ley K. Live cell imaging of paxillin in rolling neutrophils by dual-color quantitative dynamic footprinting. Microcirculation 2011; 18:361-72 Full Text | CMC Update Article.
  • Tkachenko E, Sabouri-Ghomi M, Pertz O, Kim C, Gutierrez E, Machacek M, Groisman A, Danuser G, Ginsberg MH. Protein kinase A governs a RhoA-RhoGDI protrusion-retraction pacemaker in migrating cells. Nat. Cell Biol. 2011; 13:661-8 PubMed | CMC Update Article.
  • Wang Y, Yang F, Fu Y, Huang X, Wang W, Jiang X, Gritsenko MA, Zhao R, Monore ME, Pertz OC, Purvine SO, Orton DJ, Jacobs JM, Camp DG, Smith RD, Klemke RL. Spatial phosphoprotein profiling reveals a compartmentalized extracellular signal-regulated kinase switch governing neurite growth and retraction. J. Biol. Chem. 2011; 286:18190-201 Full Text.
  • Ye F, Kim C, Ginsberg MH. Molecular mechanism of inside-out integrin regulation. J. Thromb. Haemost. 2011; 9 Suppl 1:20-5 PubMed.

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  • Hall EH, Balsbaugh JL, Rose KL, Shabanowitz J, Hunt DF, Brautigan DL. Comprehensive analysis of phosphorylation sites in Tensin1 reveals regulation by p38MAPK. Mol. Cell Proteomics 2010; 9:2853-63 PubMed | CMC Update Article.
  • Kelber JA, Klemke RL. PEAK1, a novel kinase target in the fight against cancer. Oncotarget 2010; 1:219-23 Full Text.
  • Parsons JT, Horwitz AR, Schwartz MA. Cell adhesion: integrating cytoskeletal dynamics and cellular tension. Nat. Rev. Mol. Cell Biol. 2010; 11:633-43 Full Text.
  • Tilghman RW, Cowan CR, Mih JD, Koryakina Y, Gioeli D, Slack-Davis JK, Blackman BR, Tschumperlin DJ, Parsons JT. Matrix rigidity regulates cancer cell growth and cellular phenotype. PLoS ONE 2010; 5:e12905 Full Text.
  • Wang Y, Kelber JA, Tran Cao HS, Cantin GT, Lin R, Wang W, Kaushal S, Bristow JM, Edgington TS, Hoffman RM, Bouvet M, Yates JR, Klemke RL. Pseudopodium-enriched atypical kinase 1 regulates the cytoskeleton and cancer progression [corrected]. Proc. Natl. Acad. Sci. U.S.A. 2010; 107:10920-5 Full Text | CMC Update Article.
  • Ye F, Hu G, Taylor D, Ratnikov B, Bobkov AA, McLean MA, Sligar SG, Taylor KA, Ginsberg MH. Recreation of the terminal events in physiological integrin activation. J. Cell Biol. 2010; 188:157-73 Full Text | CMC Update Article.

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  • Anthis NJ, Haling JR, Oxley CL, Memo M, Wegener KL, Lim CJ, Ginsberg MH, Campbell ID. Beta integrin tyrosine phosphorylation is a conserved mechanism for regulating talin-induced integrin activation. J. Biol. Chem. 2009; 284:36700-10 Full Text | CMC Update Article.
  • Anthis NJ, Wegener KL, Ye F, Kim C, Goult BT, Lowe ED, Vakonakis I, Bate N, Critchley DR, Ginsberg MH, Campbell ID. The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. EMBO J. 2009; 28:3623-32 Full Text | CMC Update Article.
  • Gingras AR, Ziegler WH, Bobkov AA, Joyce MG, Fasci D, Himmel M, Rothemund S, Ritter A, Grossmann JG, Patel B, Bate N, Goult BT, Emsley J, Barsukov IL, Roberts GC, Liddington RC, Ginsberg MH, Critchley DR. Structural determinants of integrin binding to the talin rod. J. Biol. Chem. 2009; 284:8866-76 Full Text.
  • Huang C, Rajfur Z, Yousefi N, Chen Z, Jacobson K, Ginsberg MH. Talin phosphorylation by Cdk5 regulates Smurf1-mediated talin head ubiquitylation and cell migration. Nat. Cell Biol. 2009; 11:624-30 Full Text | CMC Update Article.
  • Hunt, D, Jeffery, ED. Full Protein Sequence Mapping using Mass Spectrometry. Nature Protocols (on line) 2009; DOI.
  • Hunt, D, Jeffery, ED. Full protein sequence mapping using mass spectrometry. Nature Protocols (on line) 2009; doi:10.1038/nprot.2009.50: DOI.
  • Lee HS, Lim CJ, Puzon-McLaughlin W, Shattil SJ, Ginsberg MH. RIAM activates integrins by linking talin to ras GTPase membrane-targeting sequences. J. Biol. Chem. 2009; 284:5119-27 Full Text.

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  • Lim CJ, Kain KH, Tkachenko E, Goldfinger LE, Gutierrez E, Allen MD, Groisman A, Zhang J, Ginsberg MH. Integrin-mediated protein kinase A activation at the leading edge of migrating cells. Mol. Biol. Cell 2008; 19:4930-41 Full Text | CMC Update Article.
  • Pertz OC, Wang Y, Yang F, Wang W, Gay LJ, Gristenko MA, Clauss TR, Anderson DJ, Liu T, Auberry KJ, Camp DG, Smith RD, Klemke RL. Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network. Proc. Natl. Acad. Sci. U.S.A. 2008; 105:1931-6 Full Text.
  • Seward ME, Easley CA, McLeod JJ, Myers AL, Tombes RM. Flightless-I, a gelsolin family member and transcriptional regulator, preferentially binds directly to activated cytosolic CaMK-II. FEBS Lett. 2008; 582:2489-95 PubMed.
  • Sherman, N, Fox, JW. Identification of Utilized Phosphorylation Sites in Tagged Proteins. Nature Protocols (on line) 2008; doi: 10.1038/nprot.2008.202: DOI.
  • Wang Y, Klemke RL. PhosphoBlast, a computational tool for comparing phosphoprotein signatures among large datasets. Mol. Cell Proteomics 2008; 7:145-62 PubMed | CMC Update Article.

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  • Chi A, Bai DL, Geer LY, Shabanowitz J, Hunt DF. Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. Int J Mass Spectrom 2007; 259:197-203 Full Text.
  • Goldfinger LE, Ptak C, Jeffery ED, Shabanowitz J, Han J, Haling JR, Sherman NE, Fox JW, Hunt DF, Ginsberg MH. An experimentally derived database of candidate Ras-interacting proteins. J. Proteome Res. 2007; 6:1806-11 PubMed | CMC Update Article.
  • Hunt, D, Jeffery, ED. Method for Full Protein Sequence Mapping: LC-MS analysis. Nature Protocols (on line) 2007; doi: 10.1038/nprot.2007.34: DOI.
  • Hunt, D, Jeffery, ED. Method for Full Protein Sequence Mapping: LC-MS sample preparation. Nature Protocols (on line) 2007; doi: 10.1038/nprot.2007.33: DOI.
  • Jeffery, ED. Method for full protein sequence mapping: LC-MS sample preparation. Nature Protocols (on line) 2007; doi:10.1038/nprot.2007.33: DOI.
  • Lim CJ, Han J, Yousefi N, Ma Y, Amieux PS, McKnight GS, Taylor SS, Ginsberg MH. Alpha4 integrins are type I cAMP-dependent protein kinase-anchoring proteins. Nat. Cell Biol. 2007; 9:415-21 PubMed.
  • Mayhew MW, Jeffery ED, Sherman NE, Nelson K, Polefrone JM, Pratt SJ, Shabanowitz J, Parsons JT, Fox JW, Hunt DF, Horwitz AF. Identification of phosphorylation sites in betaPIX and PAK1. J. Cell. Sci. 2007; 120:3911-8 PubMed | CMC Update Article.
  • Petrich BG, Fogelstrand P, Partridge AW, Yousefi N, Ablooglu AJ, Shattil SJ, Ginsberg MH. The antithrombotic potential of selective blockade of talin-dependent integrin alpha IIb beta 3 (platelet GPIIb-IIIa) activation. J. Clin. Invest. 2007; 117:2250-9 Full Text | CMC Update Article.
  • Petrich BG, Marchese P, Ruggeri ZM, Spiess S, Weichert RA, Ye F, Tiedt R, Skoda RC, Monkley SJ, Critchley DR, Ginsberg MH. Talin is required for integrin-mediated platelet function in hemostasis and thrombosis. J. Exp. Med. 2007; 204:3103-11 Full Text | CMC Update Article.
  • Prager GW, Féral CC, Kim C, Han J, Ginsberg MH. CD98hc (SLC3A2) interaction with the integrin beta subunit cytoplasmic domain mediates adhesive signaling. J. Biol. Chem. 2007; 282:24477-84 PubMed.
  • Udeshi ND, Shabanowitz J, Hunt DF, Rose KL. Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS. FEBS J. 2007; 274:6269-76 PubMed.
  • Wang Y, Ding SJ, Wang W, Jacobs JM, Qian WJ, Moore RJ, Yang F, Camp DG, Smith RD, Klemke RL. Profiling signaling polarity in chemotactic cells. Proc. Natl. Acad. Sci. U.S.A. 2007; 104:8328-33 Full Text | CMC Update Article.
  • Wang Y, Ding SJ, Wang W, Yang F, Jacobs JM, Camp D, Smith RD, Klemke RL. Methods for pseudopodia purification and proteomic analysis. Sci. STKE 2007; 2007:pl4 PubMed | CMC Update Article.
  • Wegener KL, Partridge AW, Han J, Pickford AR, Liddington RC, Ginsberg MH, Campbell ID. Structural basis of integrin activation by talin. Cell 2007; 128:171-82 PubMed | CMC Update Article.

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  • Goldfinger LE, Ptak C, Jeffery ED, Shabanowitz J, Hunt DF, Ginsberg MH. RLIP76 (RalBP1) is an R-Ras effector that mediates adhesion-dependent Rac activation and cell migration. J. Cell Biol. 2006; 174:877-88 Full Text | CMC Update Article.
  • Han J, Lim CJ, Watanabe N, Soriani A, Ratnikov B, Calderwood DA, Puzon-McLaughlin W, Lafuente EM, Boussiotis VA, Shattil SJ, Ginsberg MH. Reconstructing and deconstructing agonist-induced activation of integrin alphaIIbbeta3. Curr. Biol. 2006; 16:1796-806 PubMed | CMC Update Article.
  • Luxenburg C, Parsons JT, Addadi L, Geiger B. Involvement of the Src-cortactin pathway in podosome formation and turnover during polarization of cultured osteoclasts. J. Cell. Sci. 2006; 119:4878-88 PubMed | CMC Update Article.
  • Martin KH, Jeffery ED, Grigera PR, Shabanowitz J, Hunt DF, Parsons JT. Cortactin phosphorylation sites mapped by mass spectrometry. J. Cell. Sci. 2006; 119:2851-3 PubMed.
  • Mayhew MW, Webb DJ, Kovalenko M, Whitmore L, Fox JW, Horwitz AF. Identification of protein networks associated with the PAK1-betaPIX-GIT1-paxillin signaling complex by mass spectrometry. J. Proteome Res. 2006; 5:2417-23 PubMed | CMC Update Article.
  • Nayal A, Webb DJ, Brown CM, Schaefer EM, Vicente-Manzanares M, Horwitz AR. Paxillin phosphorylation at Ser273 localizes a GIT1-PIX-PAK complex and regulates adhesion and protrusion dynamics. J. Cell Biol. 2006; 173:587-9 Full Text | CMC Update Article.
  • Pertz O, Hodgson L, Klemke RL, Hahn KM. Spatiotemporal dynamics of RhoA activity in migrating cells. Nature 2006; 440:1069-72 PubMed | CMC Update Article.
  • Wang Y, Hanley R, Klemke RL. Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer. J. Proteome Res. 2006; 5:907-15 PubMed | CMC Update Article.
  • Webb DJ, Kovalenko M, Whitmore L, Horwitz AF. Phosphorylation of serine 709 in GIT1 regulates protrusive activity in cells. Biochem. Biophys. Res. Commun. 2006; 346:1284-8 PubMed | CMC Update Article.
  • Webb DJ, Mayhew MW, Kovalenko M, Schroeder MJ, Jeffery ED, Whitmore L, Shabanowitz J, Hunt DF, Horwitz AF. Identification of phosphorylation sites in GIT1. J. Cell. Sci. 2006; 119:2847-50 PubMed | CMC Update Article.

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  • Coon JJ, Shabanowitz J, Hunt DF, Syka JE. Electron transfer dissociation of peptide anions. J. Am. Soc. Mass Spectrom. 2005; 16:880-2 PubMed.
  • Coon JJ, Ueberheide B, Syka JE, Dryhurst DD, Ausio J, Shabanowitz J, Hunt DF. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2005; 102:9463-8 Full Text.
  • Garcia BA, Shabanowitz J, Hunt DF. Analysis of protein phosphorylation by mass spectrometry. Methods 2005; 35:256-64 PubMed.
  • Grigera PR, Jeffery ED, Martin KH, Shabanowitz J, Hunt DF, Parsons JT. FAK phosphorylation sites mapped by mass spectrometry. J. Cell. Sci. 2005; 118:4931-5 PubMed | CMC Update Article.
  • Nishiya N, Kiosses WB, Han J, Ginsberg MH. An alpha4 integrin-paxillin-Arf-GAP complex restricts Rac activation to the leading edge of migrating cells. Nat. Cell Biol. 2005; 7:343-52 PubMed.
  • Ratnikov B, Ptak C, Han J, Shabanowitz J, Hunt DF, Ginsberg MH. Talin phosphorylation sites mapped by mass spectrometry. J. Cell. Sci. 2005; 118:4921-3 PubMed | CMC Update Article.
  • Schroeder MJ, Webb DJ, Shabanowitz J, Horwitz AF, Hunt DF. Methods for the detection of paxillin post-translational modifications and interacting proteins by mass spectrometry. J. Proteome Res. 2005; 4:1832-41 PubMed | CMC Update Articles: 1, 2.
  • Vicente-Manzanares M, Webb DJ, Horwitz AR. Cell migration at a glance. J. Cell. Sci. 2005; 118:4917-9 PubMed | CMC Update Article.
  • Webb DJ, Schroeder MJ, Brame CJ, Whitmore L, Shabanowitz J, Hunt DF, Horwitz AR. Paxillin phosphorylation sites mapped by mass spectrometry. J. Cell. Sci. 2005; 118:4925-9 PubMed | CMC Update Article.

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  • Burridge K, Wennerberg K. Rho and Rac take center stage. Cell 2004; 116:167-79 PubMed.
  • Calderwood DA, Tai V, Di Paolo G, De Camilli P, Ginsberg MH. Competition for talin results in trans-dominant inhibition of integrin activation. J. Biol. Chem. 2004; 279:28889-95 PubMed.
  • Kloeker S, Major MB, Calderwood DA, Ginsberg MH, Jones DA, Beckerle MC. The Kindler syndrome protein is regulated by transforming growth factor-beta and involved in integrin-mediated adhesion. J. Biol. Chem. 2004; 279:6824-33 PubMed.
  • Peterson LJ, Rajfur Z, Maddox AS, Freel CD, Chen Y, Edlund M, Otey C, Burridge K. Simultaneous stretching and contraction of stress fibers in vivo. Mol. Biol. Cell 2004; 15:3497-508 Full Text.
  • Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004; 101:9528-33 Full Text.

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  • Calderwood DA, Fujioka Y, de Pereda JM, García-Alvarez B, Nakamoto T, Margolis B, McGlade CJ, Liddington RC, Ginsberg MH. Integrin beta cytoplasmic domain interactions with phosphotyrosine-binding domains: a structural prototype for diversity in integrin signaling. Proc. Natl. Acad. Sci. U.S.A. 2003; 100:2272-7 Full Text.
  • García-Alvarez B, de Pereda JM, Calderwood DA, Ulmer TS, Critchley D, Campbell ID, Ginsberg MH, Liddington RC. Structural determinants of integrin recognition by talin. Mol. Cell 2003; 11:49-58 PubMed.
  • Goldfinger LE, Han J, Kiosses WB, Howe AK, Ginsberg MH. Spatial restriction of alpha4 integrin phosphorylation regulates lamellipodial stability and alpha4beta1-dependent cell migration. J. Cell Biol. 2003; 162:731-41 Full Text.
  • Hansen M, Prior IA, Hughes PE, Oertli B, Chou FL, Willumsen BM, Hancock JF, Ginsberg MH. C-terminal sequences in R-Ras are involved in integrin regulation and in plasma membrane microdomain distribution. Biochem. Biophys. Res. Commun. 2003; 311:829-38 PubMed.
  • Kinbara K, Goldfinger LE, Hansen M, Chou FL, Ginsberg MH. Ras GTPases: integrins' friends or foes?. Nat. Rev. Mol. Cell Biol. 2003; 4:767-76 PubMed.
  • Tadokoro S, Shattil SJ, Eto K, Tai V, Liddington RC, de Pereda JM, Ginsberg MH, Calderwood DA. Talin binding to integrin beta tails: a final common step in integrin activation. Science 2003; 302:103-6 PubMed.

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  • Schwartz MA, Ginsberg MH. Networks and crosstalk: integrin signalling spreads. Nat. Cell Biol. 2002; 4:E65-8 PubMed.
  • Woodside DG, Obergfell A, Talapatra A, Calderwood DA, Shattil SJ, Ginsberg MH. The N-terminal SH2 domains of Syk and ZAP-70 mediate phosphotyrosine-independent binding to integrin beta cytoplasmic domains. J. Biol. Chem. 2002; 277:39401-8 PubMed.
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Software

BlastPro

  • BlastPro software, is a powerful new data mining tool that facilitates comparison of large proteomic and genomic datasets across species, database, and platform. This is now available for download here (readme.txt). This software is described in detail in Wang Y, Hanley R, Klemke RL. 2006 Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer. J Proteome Res. 5(4):907-15. PubMed

PhosphoBlast

  • PhosphoBlast is a program that can rapidly match thousands of phosphopeptides that share phosphorylation sites within and across species. It was developed to identify the "phosphoprotein signatures" shared among large phosphoprotein databases, in the hopes of providing valuable insight into mechanisms of signal transduction and cell function. Additionally, it is a powerful analysis tool for identifying specific phosphosite mutations. The software is described in detail in Wang Y, Klemke RL. PhosphoBlast, a computational tool for comparing phosphoprotein signatures among large datasets. Mol. Cell Proteomics 2008; 7:145-62 PubMed. It is available by contacting Dr. Wang at yingchunw2008@gmail.com.
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