RNA Epitranscriptomics and Proteomics Resource

• Up to 100,000 resolution
• Capable of HCD or CID fragmentation and MSn, DDA types of analysis

• Ultimate Mass Accuracy (ppb) and resolution (> 4 millions)
• CID, ECD, IRMPD and ETD activation
• CASI for low abundant species
• Ideal for top-down analysis

• Fast and sensitive
• Fast polarity switching
• MRM, MRM³ capabilities

• Resolution of up to 10,000
• Extended MS and MS/MS mass range (6,000 and 40,000 m/z)

• Mass accuracy within 2 ppm
• Wide in-spectrum dynamic range facilitates simultaneous measurement of minor components in the presence of intense background interferents
• Infinity UHPLC chromatographic interfaces for fast acquisition
• MassHunter software supports profiling, characterization, identification and quantification of compounds in complex mixtures via high-definition MS and MS/MS
• All Ions MS/MS enables targeted screening and quantification

• High sensitivity simplifies sample preparation and LC method development
• Jet Stream source enables sub-picogram detection limits
• Ultrafast scan speeds takes full advantage of UHPLC separations
• Isotopic resolution at 10,000 u/sec helps confirm compound identity in fast chromatography with accurate isotopic ratios
• Infinity II UHPLC chromatographic interfaces affords fast acquisition speed
• Additional detectors provide versatility by combining DAD, ELSA, and MS for extra confidence in compound purity assessment
• Walkup Software facilitates easy-to-manage, open access operation by multiple users

• Supports the most demanding quantitative UPLC-MS/MS applications and accelerates method development for sensitive and robust methods.
• High-performance ZSpray dual-orthogonal API source
• T-wave system enables optimal MS/MS performance at high data acquisition rates
• Automated MRM scheduling
• Up to 16,384 MRM channels (512 functions, 32 channels per function)
• Acquity UPLC, MassLynx software

• Combines exact mass, high resolution, mass spectrometry with high-efficiency ion-mobility-based measurements and separations
• T-wave ion mobility
• Mass-selected time-resolved (MaSTeR) fragmentation
• Time aligned parallel (TAP) dissociation

Yes, The resource offers five different platforms for self-service analysis:

1. Agilent SQ single-quadrupole.
2. Agilent QTOF quadrupole-time of flight.
3. Sciext Q-Trap quadrupole-ion trap.
4. Sciext Q-Star quadrupole-time of flight.
5. Thermo LTQ-Orbitrap Velos.

You are invited to use the Service Selection app, which enables the selection of the desired platform and provides a possible cost estimate. Then email us at [email protected] to schedule proper training on the selected platform. After completing the training, you will receive a username and password to access the instrument scheduling system.

Yes, self-service analysis is cheaper than full-service analysis.
 

Use the Service Selection app to obtain an estimate of the costs for instrument time. Make sure to review the Instrument Usage Policies provided during training.

Yes, the resource is set up to provide confidential service to private corporations. If required, we can sign material transfer agreements, non-disclosure agreements, and any other type of legal document. Email us at [email protected] with any questions you may have about this type of service.

No, REPR is open for business with any type of academic, government or private entity. Please email us at [email protected] if you have any questions about our services.

No, The VPR’s Office and the Dean of Arts and Sciences fund the salary of REPR’s personnel, but instrument operations, upkeep, and consumables are paid by cost recharges. If you have financial constraints, there are different mechanisms at UAlbany to provide seed money to generate preliminary data for grant applications. If interested, please email us at [email protected].

The mission of REPR is to primarily support the research and scholarship of UAlbany Faculty, although collaborations with selected extramural investigators are also encouraged. Due to budget constraints, REPR prioritizes long-term relationships/projects over short-term service with no intellectual participation/commitment. To this effect, REPR is involved in project planning, generating preliminary data, helping with grant writing, and carrying out project activities after funding is secured. This type of involvement requires arrangements in which the pre-award REPR contributions are supported by startup, seed money, or other funding sources, whereas the post-award activities are covered by the grant’s budget. If you are interested in learning more about these types of arrangements, please email us at [email protected].

The full-service option involves a modicum of help with experiment planning and data interpretation. If more time is necessary, REPR offers consulting services for very reasonable rates. Self-service analysis involves initial training, which is provided for a modest fee. During training, the instructor provides basic information on how to plan an experiment and perform data interpretation. Make sure to approach the training sessions with a specific project in mind, so that you can ask the most pertinent questions. If interested in learning more, use the Service Selection app to learn the going rates for consulting and training, or email us at [email protected].

Yes, we do, but on a limited basis. Due to personnel and budget constraints, we are limited on the type of operations that we can carry out, and on the number of samples that we can process. REPR encourages users to submit MS-ready samples, which can be readily analyzed by either direct infusion or LC-MS techniques. The Recommended Protocols provide a series of Standard Operating Procedures (SOPs) with instructions on how to best prepare the samples for immediate analysis. You can find the Recommended Protocols on the Services and Instrumentation tab.

If the desired type of sample is not covered, if you have questions on how to perform SOP procedures, or would like to know if REPR personnel can do sample preparation for you, please email us at [email protected].

Core Staff Publications

1. 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.
2. 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.
3. 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.
    

Core User Publications

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. 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.
4. 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.
5. 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.
6. 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
7. 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.
8. Burz, D. S., & Shekhtman, A. 2008. In-cell biochemistry using NMR spectroscopy. PLoS One, 3(7): e2571.

Core Staff Publications

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. 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.
    

Core User Publications

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
    

Core Staff Publications

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.
    

Core User Publications

1. 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.
2. 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.
3. 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.
   
    

Core User Publications

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.
    

Core User Publications

1. 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.

Core Staff Publications

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. 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.
3. 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.
4. Zisman, L. S., Keller, R. S., Weaver, B., Lin, Q., Speth, R., Bristow, M. R., & Canver, C. C. 2003. Increased angiotensin-(1-7)-forming activity in failing human heart ventricles: evidence for upregulation of the angiotensin-converting enzyme Homologue ACE2. Circulation, 108(14): 1707-1712.
5. 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.
    

Core User Publications

1. 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.
2. 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