Proteomics & Mass Spec: Publications & Applications

The publications listed below include work performed by the Proteomics and Mass Spec Core Facility. Core Facility personnel are denoted in bold.

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. Zeng, G., Wang, Y. M., & Wang, Y. 2012.
    Cdc28-Cln3 phosphorylation of Sla1 regulates actin patch dynamics in different modes of fungal growth.
    Mol Biol Cell, 23(17): 3485-3497

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

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

  12. 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. Bai, Y., Yang, J., Zarrella, T. M., Zhang, Y., Metzger, D. W., & Bai, G. 2014.
    Cyclic Di-AMP Impairs Potassium Uptake Mediated by a Cyclic Di-AMP Binding Protein in Streptococcus pneumoniae.
    J Bacteriol., 196(3): 614-623.

  2. Yu, D., Wowor, A. J., Cole, J. L., & Kendall, D. A. 2013.
    Defining the Escherichia coli SecA dimer interface residues through in vivo site-specific photo-cross-linking
    J Bacteriol., 195(12): 2817-2825.

  3. Heng Lu, Qishan Lin, and Jihe Zhao 2013.
    Identification of Signaling Protein Complexes by Parallel Affinity Precipitation Coupled with Mass Spectrometry
    Cell Communication Insights, 2013:5 1-7 doi: 10.4137/CCI.S12484

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

Metabolomics/ Small Molecular Analysis

  1. Hong-Yu Lin, Joseph A. Haegele, Michael T. Disare, Qishan Lin, & Yimon Aye. 2015
    A Generalizable Platform for Interrogating Target- and Signal-Specific Consequences of Electrophilic Modifications in Redox-Dependent Cell Signaling.
    J. Am. Chem. Soc., 137(19), pp 6232–6244

  2. Gao, S., Chen, W., Peng, Z., Li, N., Su, L., Lv, D., Li, L., Lin, Q., Dong, X., Guo, Z., & Lou, Z. 2015.
    Urinary metabonomics elucidate the therapeutic mechanism of Orthosiphon stamineus in mouse crystal-induced kidney injury.
    J Ethnopharmacol, 166: 323-332.

  3. Brecher, M. B., Li, Z., Zhang, J., Chen, H., Lin, Q., Liu, B., & Li, H. 2014.
    Refolding of a Fully functional flavivirus methyltransferase revealed that S-adenosyl methionine but not S-adenosyl homocysteine is copurified with flavivirus methyltransferase.
    Protein Sci, 24(1): 117-128.


  • 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


  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


  1. 2016 64th ASMS meeting

  2. 2015 63rd ASMS meeting

  3. 2014 62nd ASMS meeting

  4. 2012 Bioconnex Capital Region Commercialization of Life Sciences Innovation Day

  5. ABRF 2012: learning from bio-molecules: the technology behind the story

  6. Proteomic Analysis to Understanding a Retinoid–Hypersensitive Embryonal Carcinoma Cell Mutant, MP 078, 57th ASMS Conference on Mass spectrometry and Allied Topics (2009)

  7. Proteomics/mass spectrometry shared resources

  8. 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)

  9. Northeast Region Life Sciences Core Directors Meeting (2007)

  10. ABRF 2007: Creating the Biological Roadmap

  11. Application iTRAQ Reagent for Analysis of Embryonal Carcinoma Cell line. US HUPO 2006 Second Annual Conference, Boston, Massachusetts.

  12. Neurofilament protein adduct formation

  13. Rensselaerville 2003 Conference, Rensselaerville, New York

Contact Information

Core Director

Qishan Lin, Ph.D.

(518) 591-7214


Jinghua Zhu, M.S.

(518) 591-7220