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) |
|---|---|---|---|
| bPix | Ectopic expression in HEK cells | 10 phospho-sites in 88.7% coverage of 675 aa Data available - Mayhew et al., 2007 (CMC Update Article) |
Horwitz (Hunt) |
| Calpain 2 | Ectopic expression in HEK cells | 4 phospho-sites in 88.1% coverage of 708 aa Data available |
Parsons (Fox) |
| CCM2 | 20 sites in 98.2% coverage of 444 amino acids Data available |
Ginsberg (Fox) | |
| Cortactin | Ectopic expression in HEK cells | 18 phospho-sites in 89.7% coverage of 543 aa Data available - Martin et al., 2006 |
Parsons (Hunt) |
| Dynamin 2 | Ectopic expression in HEK cells | 8 phospho-sites in 89.4% coverage of 879 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 (CMC Update Article) |
Parsons (Hunt) |
| Filamin-a | Endogenous from human platelet | 11 phospho-sites in 82.5% coverage of 2630 aa Data available |
Ginsberg (Hunt) |
| GIT1 | Ectopic expression in HEK cells | 28 phospho-sites in 89.9% coverage of 773 aa Data available - Webb et al., 2006 (CMC Update Article); Webb et al., 2006 (CMC Update Article) |
Horwitz (Hunt) |
| ICAP1 | 7 sites in 99.5% coverage of 194 amino acids Data available |
Ginsberg (Fox) | |
| Kindlin | Ectopic expression in HEK cells | 4 phospho-sites in 79.4% coverage of 645 aa Data available |
Parsons (Fox) |
| KRIT1 | 2 sites in 99.5% coverage of 735 amino acids Data available |
Ginsberg (Fox) | |
| MYH10 - (MIIB) | Ectopic expression in HEK cells | 16 sites in 79.0% coverage of 1972 amino acids Data available |
Horwitz (Hunt) |
| MYH9 - (MIIA) | Ectopic expression in HEK cells | 9 sites in 75.1% coverage of 1952 amino acids Data available |
Horwitz (Hunt) |
| Myosin light chain/MYL9 | Ectopic expression in HEK cells | 4 phospho-sites in 98.3% coverage of 172 aa Data available |
Horwitz (Hunt) |
| N-Wasp | Ectopic expression in HEK cells | 6 phospho-sites in 87.7% coverage of 505 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) |
| p130Cas | Myc-tagged and expressed in HEK cells | 9 phospho-sites in 87.0% coverage of 977 aa Data available |
Parsons (Fox) |
| Pak1 | Ectopic expression in HEK cells | 30 phospho-sites in 80.5% coverage of 529 aa Data available - Mayhew et al., 2007 (CMC Update Article) |
Horwitz |
| Parvin | Ectopic expression in HEK cells | 4 phospho-sites in 88.7% coverage of 380 aa Data available |
Parsons (Fox) |
| Paxillin | Ectopic expression in HEK cells | 38 phospho-sites in 79.4% coverage of 791 aa Data available - Schroeder et al., 2005 (CMC Update Articles: 1, 2); Webb et al., 2005 (CMC Update Article); Nayal et al., 2006 (CMC Update Article) |
Horwitz (Hunt) |
| Talin | Endogenous from human platelet | 30 phospho-sites in 95.1% coverage of 2540 aa Data available - Ratnikov et al., 2005 (CMC Update Article) |
Ginsberg (Hunt, Liddington) |
| VAV1 | Ectopic expression in HEK cells | 1 phospho-site in 86.1% coverage of 858 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) |
| Wasp | Ectopic expression in HEK cells | 8 phospho-sites in 85.8% coverage of 515 aa Data available |
Parsons (Fox) |
| Zyxin | TAP-tagged GST-Zyxin | 4 phospho-sites in 78.0% coverage of 564 aa Data available |
Hoffman, Parsons (Hunt, Beckerle) |
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Binding Partners
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Organelles
| Target Organelle | Method | Status / Publication | Contact (Collaborators) |
|---|---|---|---|
| Lamellipodium | Purification & characterization of psuedopodium phosphoproteome | 1,073 Pseudopodium-enriched and 1,088 Cell Body -enriched proteins found Data available - Wang et al., 2007 (CMC Update Article); Wang et al., 2007 (CMC Update Article); Wang and Klemke, 2008 (CMC Update Article) |
Klemke |
| Stress Fibers | stress fiber isolation protocol | 207 proteins identified in stress fibers Data available - download stress fiber analysis |
Burridge |
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Mass Spectrometry Technology Developments
| MS Technology | Status / Publication | Contact (Collaborators) |
|---|---|---|
| Differential analysis of phosphopeptide expression | Completed - Schroeder et al., 2005 (CMC Update Articles: 1, 2) | Hunt |
| ETD fragmentation improvements | Completed - ETD fragmentation - instrumentation complete Syka et al., 2004; Coon et al., 2005; Coon et al., 2005; Chi et al., 2007; Udeshi et al., 2007, software development in progress | Hunt |
| IMAC with methyl ester treatment (enhanced selection of phosphopeptides) | Completed - Garcia et al., 2005 | Hunt |
| LTQ-FTMS improvements | Completed - QLT-FTMS - instrumentation complete Syka et al., 2004 | Hunt |
| Methods for full protein sequence mapping | Completed | Hunt |