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Proteomics - Activities

Objectives

  • to develop proteomic methodologies for identifying migration related proteins, their binding partners, phosphorylation sites and post-translational modifications
  • to determine the effect of growth factor and adhesion on the binding partners, utilized phosphorylation sites and post-translational modifications for a subset of migration proteins

Phosphoproteomics | Binding Partners | Organelles | MS Technology Developments

Phosphoproteomics

Target Protein Method Status / Publication Contact (Collaborators)
Talin Endogenous from human platelet 30 phospho-sites in 95.1% coverage of 2540 aa
Data available - Ratnikov et al., 2005		 Ginsberg (Hunt, Liddington)
Pak1 Ectopic expression in HEK cells 30 phospho-sites in 80.5% coverage of 529 aa
Data available - Mayhew et al., 2007		 Horwitz
GIT1 Ectopic expression in HEK cells 28 phospho-sites in 89.9% coverage of 773 aa
Data available - Webb et al., 2006 - Webb et al., 2006		 Horwitz/Hunt
Paxillin Ectopic expression in HEK cells 38 phospho-sites in 79.4% coverage of 791 aa
Data available - CMC Update article Webb et al., 2005, Schroeder et al., 2005, Nayal et al., 2006		 Horwitz/Hunt
bPix Ectopic expression in HEK cells 10 phospho-sites in 88.7% coverage of 675 aa
Data available - Mayhew et al., 2007		 Horwitz/Hunt
Dynamin 2 Ectopic expression in HEK cells 8 phospho-sites in 89.4% coverage of 879 aa
Data available		 Parsons - (Fox)
Parvin Ectopic expression in HEK cells 4 phospho-sites in 88.7% coverage of 380 aa
Data available		 Parsons - (Fox)
Calpain 2 Ectopic expression in HEK cells 4 phospho-sites in 88.1% coverage of 708 aa
Data available		 Parsons - (Fox)
N-Wasp Ectopic expression in HEK cells 6 phospho-sites in 87.7% coverage of 505 aa
Data available		 Parsons - (Fox)
FAK Ectopic expression in HEK cells 18 phospho-sites in 80.2% coverage of 1045 aa
Data available - Grigera et al., 2005		 Parsons - (Hunt)
Cortactin Ectopic expression in HEK cells 18 phospho-sites in 89.7% coverage of 543 aa
Data available - Martin et al., 2006		 Parsons (Hunt)
alpha-Actinin Ectopic expression in HEK cells 1 phospho-site in 93.9% coverage of 905 aa
Data available		 Parsons/Fox
Vinculin Ectopic expression in HEK cells 2 phospho-sites in 92.1% coverage of 1062 aa
Data available		 Parsons/Fox
p115 Rho GEF Ectopic expression in HEK cells 15 phospho-sites in 91.7% coverage of 867 aa
Data available		 Parsons/Fox
Wasp Ectopic expression in HEK cells 8 phospho-sites in 85.8% coverage of 515 aa
Data available		 Parsons/Fox
Filamin-a Endogenous from human platelet 11 phospho-sites in 82.5% coverage of 2630 aa
Data available		 Ginsberg/Hunt
Zyxin TAP-tagged GST-Zyxin 4 phospho-sites in 78.0% coverage of 564 aa
Data available		 Parsons/Hoffman - (Hunt, Beckerle)
Kindlin Ectopic expression in HEK cells 4 phospho-sites in 79.4% coverage of 645 aa
Data available		 Parsons - (Fox)
VAV1 Ectopic expression in HEK cells 1 phospho-site in 86.1% coverage of 858 aa
Data available		 Parsons - (Fox)
p130Cas Myc-tagged and expressed in HEK cells 9 phospho-sites in 87.0% coverage of 977 aa
Data available		 Parsons - (Fox)
PINCH Ectopic expression in HEK cells in progress Parsons - (Fox)
LIMK1 Ectopic expression in HEK cells in progress Parsons - (Fox)
Gelsolin Ectopic expression in HEK cells in progress Parsons - (Fox)
Myosin II Ectopic expression in HEK cells in progress Horwitz/Hunt
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Binding Partners

Target Protein Method Status / Publication Contact (Collaborators)
R-Ras38V Ectopic expression in NIH 3T3 cells 25 co-purified proteins validated
Data available - Goldfinger et al., 2006, CMC Update article; Goldfinger et al., 2007, CMC Update article		 Ginsberg (Hunt)
Rap1A(G12V) Ectopic expression in NIH 3T3 cells 50 co-purified proteins validated
Data available - Goldfinger et al., 2007, CMC Update article		 Ginsberg (Hunt)
H-Ras 12V Ectopic expression in NIH 3T3 cells 247 co-purified proteins validated
Data available - Goldfinger et al., 2007, CMC Update article		 Ginsberg (Hunt)
Calpain 2 Ectopic expression in HEK cells Data available Horwitz
Paxillin Ectopic expression in HEK cells 10 co-purifying proteins validated
Data available - Schroeder et al., 2005 Mayhew et al., 2006		 Horwitz
Rac1 Ectopic expression in HEK cells Data available Horwitz
beta and delta isoform of CamK-II Ectopic expression in NIH 3T3 cells Data available Horwitz
Pak1 Ectopic expression in HEK cells 13 proteins exclusively co-purified with Pak1
Data available - CMC Update article Mayhew et al., 2006		 Horwitz
GIT1 Ectopic expression in HEK cells 7 proteins exclusively co-purified with Git1
Data available - CMC Update article Mayhew et al., 2006 Webb et al., 2006		 Horwitz
Pix Ectopic expression in HEK cells 7 proteins exclusively co-purified with Pix
Data available - CMC Update article Mayhew et al., 2006		 Horwitz, (Hunt)
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Organelles

Target Organelle Method Status / Publication Contact (Collaborators)
Lamellipodium Purification & characterization of psuedopodium phosphoproteome Data available - CMC Update article 1and 2 Wang & Klemke, 2008, Wang et al., 2007, Wang et al., 2007 Klemke
Stress Fibers stress fiber isolation protocol stress fiber mass spec results; download stress fiber analysis Burridge
Proteomic databases Development of computational software/methods Data available - Wang et al., 2008 Software available  
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Mass Spectrometry Technology Developments

MS Technology Status / Publication Contact (Collaborators)
Methods for full protein sequence mapping Data available Hunt
IMAC with methyl ester treatment (enhanced selection of phosphopeptides) Data available - Garcia et al., 2005 Hunt
LTQ-FTMS improvements Data available - QLT-FTMS - instrumentation complete Syka et al., 2004a Hunt
ETD fragmentation improvements Data available - ETD fragmentation - instrumentation complete Syka et al., 2004b, Coon et al., 2005, Coon et al., 2005, Udeshi et al., 2007, software development in progress Chi, et al., 2007 Hunt
Differential analysis of phosphopeptide expression Data available - Schroeder et al., 2005 Hunt
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