Ying Ge, Ph.D.

Dr. Ying GeDirector of Mass Spectrometry
Human Proteomics Program
School of Medicine and Public Health
University of Wisconsin - Madison

Education
B.S. 1997, Peking (Beijing) University, China
Ph.D. 2002, Cornell University

Contact Information
Email: yge@physiology.wisc.edu
(608) 263-9212 Phone
(608) 265-5512 Fax

Research Interests

We are interested in developing and applying cutting-edge ultra high-resolution mass spectrometry-based proteomics and metabolomics technology for biomedical research.
Specifically, my current research is focused on three major directions:

  1. Top-down disease proteomics of myofilaments - deciphering protein modifications for understanding and diagnosis of heart diseases.

  2. Label-free comparative proteomics and metabolomics for systems biology - discovery, characterization and validation of biomarkers associated with human disease.

  3. Characterization of complex post-translational modifications in large proteins (140 kDa) by high resolution tandem mass spectrometry with electron capture dissociation.

Publications at UW-Madison

  1. Oliveira, S.M.; Zhang, Y.H.; Sancho Solís, R.; Isackson, H.; Bellahcene, M.; Yavari, A.; Pinter, K.; Davies, J.D., Ge, Y.; Ashrafian, H.; Walker, J. W.; Carling, D.; Watkins, H.; Casadei, B.; Redwood, C. AMP-activated protein kinase phosphorylates cardiac troponin I and alters contractility of murine ventricular myocytes, Circ. Res., Epub ahead of print.

  2. Valkevich, E. M.; Guenette, R. G.; Sanchez, N. A.; Chen, Y.; Ge, Y.; Strieter, E. R. Forging isopeptide bonds using thiol-ene chemistry: site-specific coupling of ubiquitin molecules for studying the activity of isopeptidases, J. Am. Chem. Soc. 2012, 134, 6916-6919.

  3. Peng, Y.; Chen, X.; Sato, T., Rankin, S. A.; Tsuji, R. F.; Ge, Y. Rapid Purification and High-Resolution Top-down Mass Spectrometric Characterization of Human Salivary α-Amylase, Anal. Chem. 2012, 84, 3339-3346. (Ge, Y. Corresponding author)

  4. Du, J.; Teng, R. J.; Lawrence M.; Guan, T.; Ge, Y.; Shi, Y. The protein partners of GTP cyclohydrolase I (GCH1) in rat organs, Plos One, 2012, 7, e33991.

  5. Dong, X.; Sumandea, C. A.; Chen, Y.; Garcia-Cazarin, M. L.; Zhang, J.; Balke, C. M.; Sumandea, M. P.; Ge, Y. Augmented phosphorylation of cardiac troponin I in hypertensive heart failure, J. Biol. Chem. 2012, 287, 848-857. (Ge, Y. Corresponding author)

  6. Wang, Y.; Pinto, J. R.; Sancho Solis, R.; Liang, J.; Diaz-Perez, Z.; Harada, K.; Ge, Y.; Walker, J. W. Potter, J. D. The generation and functional characterization of knock in mice harboring the cardiac Troponin I-R21C mutation associated with hypertrophic cardiomyopathy, J. Biol. Chem. 2012, 287, 2156-2167.

  7. Zhang, H.; Ge, Y. Comprehensive analysis of protein modifications by top-down mass spectrometry, Circ. Cardiovasc. Genet. 2011, 4, 711. *This is an invited review for "Integrating proteomics into cardiovascular disease – an educational review series". (Ge, Y. Corresponding author)

  8. Zhang, J.; Guy, J. M.; Norman, H. A.; Chen, Y.; Dong, X.; Wang, S.; Kohmoto, T.; Young, K. H.; Moss, R. L.; Ge, Y. Top-Down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure, J. Proteome. Res. 2011, 10, 4054-4065. (Ge, Y. Corresponding author)

  9. Zhang, J.; Ayaz-Guner, S.; Dong, X.; Xu, Q.; Guner, H.; Ge, Y. Phosphorylation, but not alternative splicing or proteolytic degradation, is conserved in human and mouse cardiac troponin T, Biochemistry, 2011, 50, 6081-6092. (Ge, Y. Corresponding author)

  10. Sancho Solis, R.; Ge, Y.; Walker, J. W. A preferred AMPK phosphorylation site in the inhibitory loop of cardiac and skeletal troponin I, Protein Sci. 2011, 20, 894-907. (Ge, Y. Corresponding author)

  11. Kuhn, P.; Chumanov, R.; Wang, Y.; Ge, Y.; Burgess, R. R.; Xu, W. Automethylation of CARM1 allows coupling of transcription and mRNA splicing, Nucl. Acids Res. 2011, 39, 2717-2726.

  12. Xu, F.; Xu, Q.; Dong, X.; Guy, M.; Guner, H.; Hacker, T. A.; Ge, Y. Top-down high-resolution electron capture dissociation mass spectrometry for comprehensive characterization of post-translational modifications in rhesus monkey cardiac troponin I, Int. J. Mass Spectrom. 2011, 305, 95-102. *This is an invited article. (Ge, Y. Corresponding author)

  13. Nelson, C. A.; Szezech, J. R.; Dooley, C. J.; Xu, Q.; Lawrence, M. J.; Zhu, R.; Jin, S.; Ge, Y. Effective enrichment and mass spectrometry analysis of phosphopeptides using mesoporous metal oxide nanomaterials, Anal. Chem. 2010, 82, 7193-7201. (Ge, Y. Corresponding author)

  14. Zhang, J.; Dong, X.; Hacker, T. A.; Ge, Y. Deciphering modifications in swine cardiac troponin I by Top-down high-resolution tandem mass spectrometry, J. Am. Soc. Mass. Spectrom. 2010, 21, 940-948. (Ge, Y. Corresponding author) * This is an invited article featured on the cover of the journal.

  15. Ayaz-Guner, S.; Zhang, J.; Li, L.; Walker, J. W.; Ge, Y. In vivo phosphorylation site mapping in mouse cardiac troponin I by high resolution top-down electron capture dissociation mass spectrometry: Ser22/23 are the only sites basally phosphorylated, Biochemistry, 2009, 48, 8161-8170. (Ge, Y. Corresponding author)

  16. Ge, Y.; Rybakova, I.; Xu, Q.; Moss, R. L. Top-down high resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state, Proc. Natl. Acad. Sci. U. S. A. 2009,106, 12658-12663. (Ge, Y. Corresponding author) *This article is a PNAS Direct Submission (Track II).

  17. Kuhn, P.; Xu, Q.; Cline, E.; Zhang, D.; Ge, Y.; Xu, W. Delineating Anopheles gambiae coactivator associated arginine methyltransferase 1 (AgCARM1) by top-down high resolution tandem mass spectrometry, Protein Sci. 2009, 18, 1272-1280. (Ge, Y. Corresponding author)

  18. Du, J.; Wei, N; Xu, H.; Ge, Y.; Vasquez-Vivar, J.; Guan, T.; Oldham, K. T.; Pritchard, K. A.; Shi, Y. Identification and functional characterization of phosphorylation sites on GTP cyclohydrolase I, Arterioscler. Thromb. Vasc. Biol. 2009, 29, 2161-2168.

  19. Nelson, C. A.; Szczech, J. R.; Xu, Q.; Jin, S.; Ge, Y. Mesoporous Zirconium oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics, Chem. Commun. 2009, 6607-6609. (Ge, Y. Corresponding author)

  20. Liu, L.; Hou, J.; Du, J.; Chumanov, R. S.; Xu, Q.; Ge, Y.; Johnson, J.A.; Murphy, R.M. Differential modification of Cys10 alters transthyretin's effect on beta-amyloid aggregation and toxicity, Protein Eng. Des. Sel. 2009, 1–10.

  21. Ma, M.; Chen, R.; Ge, Y.; He, H; Marshall, A. G.; Li, L. Combining bottom-up and top-down mass spectrometric strategies for de novo sequencing of the Crustacean hyperglycemic hormone (CHH) from Cancer borealis, Anal. Chem. 2009, 81, 240-247.

  22. Sancho Solis, R.; Ge, Y.; Walker, J. W. Single amino acid sequence polymorphisms in rat cardiac troponin revealed by top-down tandem mass spectrometry, J. Muscle Res. Cell Motil. 2008, 29, 203-212.

  23. Zabrouskov, V.; Ge, Y.; Schwartz, J.; Walker, J. W. Unraveling molecular complexity of phosphorylated human cardiac troponin I by top down electron capture dissociation/electron transfer dissociation mass spectrometry, Mol. Cell. Proteomics 2008, 7, 1838-1849. (Ge, Y. Corresponding author)

    Publications Prior to UW-Madison

  24. Colabroy, K. L.; Zhai, H. L.; Li, T. F.; Ge, Y.; Zhang, Y.; Liu, A. M.; Ealick, S. E.; McLafferty, F. W.; Begley, T. P., The mechanism of inactivation of 3-hydroxyanthranilate-3,4-dioxygenase by 4-chloro-3-hydroxyanthranilate. Biochemistry 2005, 44, 7623-7631.

  25. Xiang, J.; Ipek, M.; Suri, V.; Massefski, W.; Pan, N.; Ge, Y.; Tam, M.; Xing, Y.; Tobin, J.; Xu, X.; Tam, S. Synthesis and biological evaluation of sulfonamidooxazoles and β-keto sulfones: selective inhibitors of 11–hydroxyster oid dehydrogenase type I, Bioorg. Med. Chem. Lett. 2005, 15, 2865-2869.

  26. Ge, Y.; Lawhorn, B. G.; ElNaggar, M.; Sze, S. K.; Begley, T. P.; McLafferty, F. W. Protein oxidation in viral prolyl-4-hydroxylase characterized by top down high resolution tandem mass spectrometry, Protein Sci. 2003, 12, 2320-2326.

  27. Ge, Y.; ElNaggar, M.; Sze, N.; Oh, H.; Begley, T. P.; McLafferty, F. W.; Boshoff, H.; Barry, C. B. Top down characterization of secreted proteins from mycobacterium tuberculosis by electron capture dissociation mass spectrometry J. Am. Soc. Mass Spectrom. 2003, 14, 253-261.

  28. Sze, S. K.; Ge, Y.; Oh, H.; McLafferty, F. W. Plasma electron capture characterization of large dissociation for the proteins by top down mass spectrometry Anal. Chem. 2003, 75, 1599-1603.

  29. Oh, H.; Bruker, K.; Sze, S. K.; Ge, Y.; McLafferty, F. W. Secondary and tertiary structure of gaseous ions characterized by electron capture dissociation mass spectrometry and photofragment spectroscopy, Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 15863-15868.

  30. Sze, S. K.; Ge, Y.; Oh, H.; McLafferty, F. W. Top down mass spectrometry of a 29 kDa protein for characterization of any posttranslational modification to within one residue, Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 1774-1779.

  31. Ge, Y.; Lawhorn, B. G.; ElNaggar, M.; Strauss, E.; Park, J-H.; Begley, T. P.; McLafferty, F. W. "Top down" characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry, J. Am. Chem. Soc. 2002, 124, 672-678.

  32. Xi, J.; Ge, Y.; Kinsland, C. L.; McLafferty, F. W.; Begley, T. P. Biosynthesis of the thiazole moiety of thiamin in Echeriachia coli: identification of a novel acyldisulfide linked protein-protein conjugate that is functionally analogous to the ubiquitin/E1 complex, Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 8513-8518.

  33. Ge, Y.; Horn, D. M.; McLafferty, F. W. Blackbody infrared radiative dissociation of larger (42 kDa) multiply charged proteins, Int. J. Mass Spectrom. 2001, 210/211, 203-214.

  34. McLafferty, F. W.; Horn, D. M.; Ge, Y.; Cerda, B.; Fridriksson, E.; Breuker, K. New frontiers in molecular mass spectrometry, Adv. Mass Spectrom. 2001, 67, 167-173.

  35. McLafferty, F. W.; Horn, D. M.; Breuker, K.; Ge, Y.; Cerda, B., A. Electron capture dissociation of gaseous multiply charged ions by FTICR, J. Am. Soc. Mass Spectrom. 2001, 12, 245-249.

  36. Strauss, E.; Kinsland, C.; Ge, Y.; McLafferty, F. W.; Begley, T. P. The identification and characterization of phosphopantothenoylcysteine synthetase from E. coli completes the identification of coenzyme a biosynthetic enzymes in bacteria, J. Biol. Chem. 2001, 276, 13513.

  37. Horn, D. M.; Ge, Y.; McLafferty, F. W. Activated ion electron capture dissociation for mass spectral sequencing for larger (42 kDa) proteins, Anal. Chem. 2000, 72, 4778-4784.