Proteomics/Mass Spectrometry

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Core related publications/applications

• Publication links in green correspond to core staff's publications
• Publication links in blue correspond to core user's publications

Phosphorylation/ Acetylation and other post translational modifications (PTMs) related

1. Rangasamy, V., Mishra, R., Sondarva, G., Das, S., Lee, T. H., Bakowska, J. C., Tzivion, G., Malter, J. S., Rana, B., Lu, K. P., Kanthasamy, A., &: Rana, A. 2012
   Mixed-lineage kinase 3 phosphorylates prolyl-isomerase Pin1 to regulate its nuclear translocation and cellular function
   Proc Natl Acad Sci U S A, 109(21): 8149-8154

2. Ganguly, A., Bhattacharya, R., & Cabral, F. 2012
   Control of MCAK degradation and removal from centromeres
   Cytoskeleton (Hoboken), 69(5): 303-311

3. Lu, H., Wang, X., Li, T., Urvalek, A. M., Yu, L., Li, J., Zhu, J., Lin, Q., Peng, X., & Zhao, J. 2011
   Identification of poly (ADP-ribose) polymerase-1 (PARP-1) as a novel Kruppel-like factor 8-interacting and -regulating protein
   J Biol Chem, 286(23): 20335-20344

4. Urvalek, A. M., Lu, H., Wang, X., Li, T., Yu, L., Zhu, J., Lin, Q., &: Zhao, J. 2011
   Regulation of the oncoprotein KLF8 by a switch between acetylation and sumoylation
   Am J Transl Res, 3(2): 121-132

5. Flott, S., Kwon, Y., Pigli, Y. Z., Rice, P. A., Sung, P., & Jackson, S. P. 2011
   Regulation of Rad51 function by phosphorylation
   EMBO Rep, 12(8): 833-839

6. Xu, D., Yao, Y., Lu, L., Costa, M., & Dai, W. 2010
   Plk3 functions as an essential component of the hypoxia regulatory pathway by direct phosphorylation of HIF-1alpha
   J Biol Chem, 285(50): 38944-38950

7. Xu, D., Yao, Y., Jiang, X., Lu, L., & Dai, W. 2010
   Regulation of PTEN stability and activity by Plk3
   J Biol Chem, 285(51): 39935-39942

8. Martinez-Rucobo, F. W., Eckhardt-Strelau, L., & Terwisscha van Scheltinga, A. C. 2009
   Yeast chitin synthase 2 activity is modulated by proteolysis and phosphorylation
   Biochem J, 417(2): 547-554

9. Ross, J. A., Nagy, Z. S., & Kirken, R. A. 2008
   The PHB1/2 phosphocomplex is required for mitochondrial homeostasis and survival of human T cells
   J Biol Chem, 283(8): 4699-4713

10. Burz, D. S., & Shekhtman, A. 2008
    In-cell biochemistry using NMR spectroscopy
    PLoS One, 3(7): e2571

11. Zheng, X. D., Lee, R. T., Wang, Y. M., Lin, Q. S., & Wang, Y. 2007
    Phosphorylation of Rga2, a Cdc42 GAP, by CDK/Hgc1 is crucial for Candida albicans hyphal growth
    EMBO J, 26(16): 3760-3769

Protein expression profiling including iTRAQ and ICAT quantitative proteomics and MudPIT

1. Dyavaiah, M., Rooney, J. P., Chittur, S. V., Lin, Q., & Begley, T. J. 2011
   Autophagy-dependent regulation of the DNA damage response protein ribonucleotide reductase 1
   Mol Cancer Res, 9(4): 462-475

2. Wei, Z., Hu, W., Lin, Q., Cheng, X., Tong, M., Zhu, L., Chen, R., & He, G. 2009
   Understanding rice plant resistance to the Brown Planthopper (Nilaparvata lugens): a proteomic approach
   Proteomics, 9(10): 2798-2808

3. Gong, Y., Lippa, C. F., Zhu, J., Lin, Q., & Rosso, A. L. 2009
   Disruption of glutamate receptors at Shank-postsynaptic platform in Alzheimer's disease
   Brain Res, 1292: 191-198

4. Luo, J., Ning, T., Sun, Y., Zhu, J., Zhu, Y., Lin, Q., & Yang, D. 2009
   Proteomic analysis of rice endosperm cells in response to expression of hGM-CSF
   J Proteome Res, 8(2): 829-837

5. McCutcheon, J. P., McDonald, B. R., & Moran, N. A. 2009
   Convergent evolution of metabolic roles in bacterial co-symbionts of insects
   Proc Natl Acad Sci U S A, 106(36): 15394-15399

6. McCutcheon, J. P., McDonald, B. R., & Moran, N. A. 2009
   Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont
   PLoS Genet., 5(7): e1000565

7. Degnan, P. H., Yu, Y., Sisneros, N., Wing, R. A., & Moran, N. A. 2009
   Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors
   Proc Natl Acad Sci U S A, 106(22): 9063-9068

8. Klees, R. F., Salasznyk, R. M., Vandenberg, S., Bennett, K., & Plopper, G. E. 2007
   Laminin-5 activates extracellular matrix production and osteogenic gene focusing in human mesenchymal stem cells
   Matrix Biol., 26(2): 106-114

9. Bennett, K. P., Bergeron, C., Acar, E., Klees, R. F., Vandenberg, S. L., Yener, B., & Plopper, G. E. 2007
   Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells
   BMC Genomics, 8: 380

10. Snelling, W. J., Lin, Q., Moore, J. E., Millar, B. C., Tosini, F., Pozio, E., Dooley, J. S., & Lowery, C. J. 2007
    Proteomics analysis and protein expression during sporozoite excystation of Cryptosporidium parvum (Coccidia, Apicomplexa)
    Mol Cell Proteomics, 6(2): 346-355

Protein structural analysis and identification

1. He, Y., Ning, T., Xie, T., Qiu, Q., Zhang, L., Sun, Y., Jiang, D., Fu, K., Yin, F., Zhang, W., Shen, L., Wang, H., Li, J., Lin, Q., Li, H., Zhu, Y., & Yang, D. 2011
   Large-scale production of functional human serum albumin from transgenic rice seeds
   Proc Natl Acad Sci U S A, 108(47): 19078-19083

2. Xu, H. Z., Huang, Y., Wu, Y. L., Zhao, Y., Xiao, W. L., Lin, Q. S., Sun, H. D., Dai, W., & Chen, G. Q. 2010
   Pharicin A, a novel natural ent-kaurene diterpenoid, induces mitotic arrest and mitotic catastrophe of cancer cells by interfering with BubR1 function
   Cell Cycle, 9(14): 2897-2907

3. Xia, K., Manning, M., Hesham, H., Lin, Q., Bystroff, C., & Colon, W. 2007
   Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE
   Proc Natl Acad Sci U S A, 104(44): 17329-17334

4. Ansong, C., Miles, S. M., & Fay, P. J. 2006
   Epitope mapping factor VIII A2 domain by affinity-directed mass spectrometry: residues 497-510 and 584-593 comprise a discontinuous epitope for the monoclonal antibody R8B12
   J Thromb Haemost, 4(4): 842-847

5. Tuo, W., Fetterer, R., Jenkins, M., & Dubey, J. P. 2005
   Identification and characterization of Neospora caninum cyclophilin that elicits gamma interferon production
   Infect Immun, 73(8): 5093-5100

6. Thyagarajan, A., & Szaro, B. G. 2004
   Phylogenetically conserved binding of specific K homology domain proteins to the 3´-untranslated region of the vertebrate middle neurofilament mRNA
   J Biol Chem, 279(48): 49680-49688

Intact Protein/DNA/RNA Molecular Weight Measurement

1. Ghosh, K. S., Pande, A., & Pande, J. 2011
   Binding of gamma-crystallin substrate prevents the binding of copper and zinc ions to the molecular chaperone alpha-crystallin
   Biochemistry, 50(16): 3279-3281

2. Banerjee, P. R., Pande, A., Patrosz, J., Thurston, G. M., & Pande, J. 2010
   Cataract-associated mutant E107A of human gammaD-crystallin shows increased attraction to alpha-crystallin and enhanced light scattering
   Proc Natl Acad Sci U S A, 108(2): 574-579

3. Pande, A., Ghosh, K. S., Banerjee, P. R., & Pande, J. 2010
   Increase in surface hydrophobicity of the cataract-associated P23T mutant of human gammaD-crystallin is responsible for its dramatically lower, retrograde solubility
   Biochemistry, 49(29): 6122-6129

4. Pande, A., Gillot, D., & Pande, J. 2009
   The cataract-associated R14C mutant of human gamma D-crystallin shows a variety of intermolecular disulfide cross-links: a Raman spectroscopic study
   Biochemistry, 48(22): 4937-4945

5. Huang, Z., Pei, W., Han, Y., Jayaseelan, S., Shekhtman, A., Shi, H., & Niu, L. 2009
   One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors
   Nucleic Acids Res, 37(12): 4022-4032

VP-ITC

• Simmons, T. J., Hashim, D., Vajtai, R., & Ajayan, P. M. 2007
  Large area-aligned arrays from direct deposition of single-wall carbon nanotube inks
  J Am Chem Soc, 129(33): 10088-10089

Others

1. Xu, H. Z., Huang, Y., Wu, Y. L., Zhao, Y., Xiao, W. L., Lin, Q. S., Sun, H. D., Dai, W., & Chen, G. Q. 2010
   Pharicin A, a novel natural ent-kaurene diterpenoid, induces mitotic arrest and mitotic catastrophe of cancer cells by interfering with BubR1 function
   Cell Cycle, 9(14): 2897-2907

2. Hulse, R. E., Swenson, W. G., Kunkler, P. E., White, D. M., & Kraig, R. P. 2008
   Monomeric IgG is neuroprotective via enhancing microglial recycling endocytosis and TNF-alpha
   J Neurosci, 28(47): 12199-12211

3. Cismasiu, V. B., Adamo, K., Gecewicz, J., Duque, J., Lin, Q., & Avram, D. 2005
   BCL11B functionally associates with the NuRD complex in T lymphocytes to repress targeted promoter
   Oncogene, 24(45): 6753-6764

4. Yoon, D. S., Han, Y., Stark, T. M., Haber, J. C., Gregg, B. T., & Stankovich, S. B. 2004
   Efficient synthesis of 4-aminoquinazoline and thieno[3,2-d]pyrimidin–4–ylamine derivatives by microwave irradiation
   Org Lett, 6(25): 4775-4778

5. Lin, Q., Keller, R. S., Weaver, B., & Zisman, L. S. 2004
   Interaction of ACE2 and integrin beta1 in failing human heart
   Biochim Biophys Acta, 1689(3): 175-178

6. Zisman, L. S., Keller, R. S., Weaver, B., Lin, Q., Speth, R., Bristow, M. R., & Canver, C. C. 2003
   Increased angiotensin–&p(1-7)–forming activity in failing human heart ventricles: evidence for upregulation of the angiotensin–converting enzyme Homologue ACE2
   Circulation, 108(14): 1707-1712

7. Lin, Q., Higgs, H. N., & Glomset, J. A. 2000
   Membrane lipids have multiple effects on interfacial catalysis by a phosphatidic acid–preferring phospholipase A1 from bovine testis
   Biochemistry, 39(31): 9335-9344

Technical Notes

1. Phosphorylation site mapping
2. Application Titanium Dioxide IMAC for Enrichment Phosphopeptides Prior to Tandem Mass spectrometry

Presentations

1. Rensselaerville 2003 Conference, Rensselaerville, New York
2. Neurofilament protein adduct formation
3. Application iTRAQ Reagent for Analysis of Embryonal Carcinoma Cell line. US HUPO 2006 Second Annual Conference, Boston, Massachusetts.
4. ABRF 2007: Creating the Biological Roadmap
5. Northeast Region Life Sciences Core Directors Meeting (2007)
6. Determination of Vincristine and Vinblastine in C. Roseus Leaves by Liquid Chromatography Mass Spectrometry, WP278, 56th ASMS Conference on Mass Spectrometry and Allied Topics(2008)
7. Proteomics/mass spectrometry shared resources
8. Proteomic Analysis to Understanding a Retinoid-Hypersensitive Embryonal Carcinoma Cell Mutant, MP 078, 57th ASMS Conference on Mass spectrometry and Allied Topics (2009)
9. ABRF 2012: learning from bio-molecules: the technology behind the story
10. 2012 Bioconnex Capital Region Commercialization of Life Sciences Innovation Day

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