Welcome to Ge Research Group!

The Ge lab at UW-Madison aims to understand the molecular and cellular mechanisms underlying cardiovascular diseases via systems biology approaches featuring cutting-edge high-resolution mass spectrometry (MS)-based comparative proteomics and metabolomics in conjunction with biochemical/biological/physiological functional studies.


Ying Ge, PhD

Associate Professor, Department of Cell and Regenerative Biology
Associate Professor, Department of Chemistry
Director of Mass Spectrometry
Human Proteomics Program
School of Medicine and Public Health
University of Wisconsin-Madison
Biographical Sketch

Faculty trainer, Translational Cardiovascular Science Training Program
Faculty trainer, Chemistry-Biology Interface Training Program
Faculty trainer, UW Graduate Program in Cellular and Molecular Biology
Faculty trainer, UW Graduate Program in Molecular and Cellular Pharmacology
Faculty trainer, UW Graduate Program in Cellular and Molecular Pathology

    News and Updates

  • April 2019, Andreas Kyrvasilis was awarded the sophomore research scholarship. Congratulations!
  • April 2019, Kyle Brown's paper on a photocleavable surfactant for top-down proteomics is published in Nature Methods! [Article] [News Release]
  • April 2019, Bifan received the Gary Parr Memorial Award! Congratulations!
  • April 2019, Abe is awarded the Doban Mentoring Award! Congratulations!
  • April 2019, Morgan received the Eugene and Patricia Kreger Herscher Scholarship, the Henry and Eleanor Firminhac Chemistry Scholarship, and the Margaret McLean Bender Scholarship!
  • Feburary 2019, Trisha Tucholski is awarded the 2019 ASMS (American Society for Mass Spectrometry) Graduate Student Travel Award. Congratulations!
  • January 2019, The Ge Lab celebrated a Holiday Party! [Photos]

  • December 2018, Benjamin Wancewicz, a Cellular and Molecular Pathology student, joined the Ge Lab. Welcome Ben!
  • December 2018, David Roberts won the Best Poster Award at the 24th Annual University of Wisconsin SMPH Cardiovascular Research Center Scientific Poster Fair. Congratulations David!
  • November 2018, First year chemistry students Elizabeth Bayne, Austin Carr, Eli Larson, and Jake Melby joined the Ge Lab. Welcome and Congratulations!
  • September 2018, Kent Wenger joined the Ge Group as a software developer on the MASH Project. Welcome!
  • August 2018, The Ge Group attended the 2018 Wisconsin Human Proteomics Symposium. [ Photos]
  • August 2018, The Ge Group celebrated everyone's hard work and the new graduate with a summer party at Ying's house! [ Photos]
  • June 2018, Members of the Ge Group attended the 66th Annual ASMS Conference. [Photos]
  • June 2018, Medical students Daniel Belongia and Max Wrobbel joined the group and each received Shapiro Summer Research Fellowships. Welcome!
  • March 2018, Wenxuan Cai is awarded with the 2018 ASMS (American Society for Mass Spectrometry) Graduate Student Travel Award. Congratulations!
  • March 2018, Dr. Yanlong Zhu is awarded with the ASMS Postdoctoral Career Development Awards. Congratulations!
  • March 2018, Undergraduate student Paige Pistono has received the Biochemistry Undergraduate Summer Research Scholarship. Congratulations!
  • January 2018, Bifan Chen won the 2018 CACA Student Excellence Awards in Chromatography. Congratulations!
  • Anouncement: 2018 Wisconsin Human Proteomics Symposium will be offered by the Human Proteomics Program at UW-Madison and the BioPharmaceutical Technology Center Institute on August 10, 2018. [Link]

  • December 2017, Wenxuan (Vege) Cai won UW-Madison Cardiovascular Research Center (CVRC) poster award. Congratulations!
  • December 2017, Stanford Mitchell, first year Molecular and Cellular Pharmacology student joined the group. Welcome!
  • November 2017, Bifan Chen won CPSA USA 2017 Steven A. Hofstadler Graduate Student award. Congratulations!
  • August 22, 2017, Zachery Gregorich passed his doctoral defense. Congratulations to Dr. Gregorich! [Photos]
  • August 19, 2017, the Ge Group enjoyed the summer picnic in Devil's Lake State Park. [Photos]
  • August 6, 2017, the Ge Group enjoyed the summer group party in Ying's house. [Photos]
  • June 2017, the Ge Group attended the 65th ASMS conference in Indianapolis, IN. [Photos]
  • June 2017, Wenxuan (Vege) Cai, a 3rd year Molecular and Cellular Pharmacology (MCP) graduate student, was awarded a highly competitive American Heart Association Pre-doctoral fellowship. Congrats Vege!
  • April 13, 2017, Hannah Karp has received the Hilldale research fellowship. Congrats Hannah!
  • March 30, 2017, Hannah Karp has received the Mary Shine Peterson Undergraduate Award. Congrats Hannah!
  • March 17, 2017, Samantha Knott (first year Chembio student) is awarded NSF graduate student fellowship! Congrats to Sam!
  • Mar. 2017, Bifan Chen is awarded with the 2017 ASMS (American Society for Mass Spectrometry) Graduate Student Award. Congratulations!
  • Feb. 1, 2017, Trisha Tucholski is awarded a National Institutes of Health (NIH) Chemistry-Biology Interface Training Program (CBI) Traineeship. Congrats Trisha!

Most Recent Publications

  1. Brown, K. A.; Chen, B.; Guardado-Alvarez, T. M.; Lin, Z.; Hwang, L.; Ayaz-Guner, S.; Jin, S.; Ge, Y. A Photocleavable Surfactant for Top-Down Proteomics, Nature Methods. 2019. Article. News Release.
  2. Jin, Y.; Diffee, G. M.; Colman, R. J.; Anderson, R. M.; Ge, Y. Top-down Mass Spectrometry of Sarcomeric Protein Post-translational Modifications from Non-human Primate Skeletal Muscle, J. Am. Soc. Mass Spectrom. 2019. Epub ahead of print. DOI: 10.1007/s13361-019-02139-0 Article
  3. Tucholski, T.; Knott, S.; Chen, B.; Pistono, P.; Lin, Z.; Ge, Y. A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Anal Chem., 2019, 91, 3855-3844. DOI: 10.1021/acs.analchem.8b04082. Article
  4. Liang, Y.; Jin, Y.; Wu, Z.; Tucholski, T.; Brown, K.A.; Zhang, L.; Zhang, Y.; Ge, Y. Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-down Proteomics, Anal Chem., 2019, 91, 3, 1743-1747. DOI: 10.1021/acs.analchem.8b05817. Article
  5. Gregorich, Z.R.; Patel, J.R.; Cai, W.; Lin, Z.; Heurer, R.; Fitzsimons, D.P.; Moss, R.L.; Ge, Y. Deletion of Enigma Homologue from the Z-disc slows tension development kinetics in mouse myocardium, J Gen Physiol., 2019. PII: jgp.201812214. DOI: 10.1085/jgp.201812214. Article
  6. Berry, J.L.; Zhu, W.; Tang, Y.L.; Krishnamurthy, P.; Ge, Y.; Cooke, J.P.; Chen, Y.; Garry, D.J.; Yang, H.T.; Rajasekaran, N.S.; Koch, W.J.; Li, S., Domae, K.; Qin, G.; Cheng, K.; Kamp, T.J.; Ye, L.; Hu, S.; Ogle, B.M.; Rogers, J.M.; Abel, E.D.; Davis, M.E.; Prabhu, S.D.,; Liao, R.; Pu, W.T.; Wang, Y.; Ping, P.; Bursac, N.; Vunjak-Novakovic, G.; Wu, J.C.; Bolli, R.; Menasché, P.; Zhang, J. Convergences of Life Sciences and Engineering in Understanding and Treating Heart Failure, Circ Res., 2019, 124, 1, 161-169. DOI: 10.1161/CIRCRESAHA.118.314216. Article
  7. Lin, Z.; Wei, L.; Cai, W.; Zhu, Y.; Tucholski, T.; Mitchell, S.D.; Guo, W.; Ford, S.P.; Diffee, G.M.; Ge, Y. Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of Sarcomeric Subproteome, Mol Cell Proteomics., 2019, 18, 3, 594-605. PII: mcp.TIR118.001086. DOI: 10.1074/mcp.TIR118.00108. Article
  8. Jin, Y.; Lin, Z.; Xu, Q.; Fu, C.; Zhang, Z.; Zhang, Q.; Pritts, W.A.; Ge, Y. Comprehensive characterization of monoclonal antibody by Fourier transform ion cyclotron resonance mass spectrometry, MAbs., 2019, 11, 1, 106-115. DOI: 10.1080/19420862.2018.1525253. Article
  9. Chen, Z.; Maimaiti, R.; Zhu, C.; Cai, H.; Stern, A.; Mozdziak, P.; Ge, Y.; Ford, S.P.; Nathanielsz P.W.; Guo, W.; Z- band and M-band titin splicing and regulation by RNA binding motif 20 in striated muscles, J. Cell Biochem., 2018, 119, 12, 9986-9996. DOI: 10.1002/jcb.27328. Article
  10. Cai, W.; Hite, Z.L.; Lyu, B.; Wu, Z.; Lin, Z.; Gregorich, Z. R.; Messer, A.E.; McIlwain, S.J.; Marston, S.B.; Kohmoto, T.; Ge, Y. Temperature-sensitive sarcomeric protein post-translational modifications revealed by top-down proteomics, J. Mol. Cell Cardiol., 2018, 122, 11-22. DOI: 10.1016/j.yjmcc.2018.07.247 Article
  11. Chen, B.; Lin, Z.; Alpert, A. J.; Fu, C.; Zhang, Q.; Pritts, W. A.; Ge, Y. Online hydrophobic interaction chromatography-mass spectrometry for the analysis of intact monoclonal antibodies, Anal. Chem., 2018 , 90, 12, 7135-7138 DOI:10.1021/acs.analchem.8b01865 Article
  12. Martin-Garrido, A.; Biesiadecki, B.J.; Salhi, H.E.; Shaifta, Y.; dos Remedios, C.G.; Ayuz-Guner, S.; Cai, W.; Ge, Y.; Avkiran, M.; Kentish, J.C., Monophosphorylation of cardiac troponin-I at Ser23/24 is sufficient to regulate cardiac myofibrillar Ca2+ sensitivity and calpain-induced proteolysis, J. Biol. Chem., 2018 , 293, 22, 8588-8599, DOI:10.1074/jbc.RA117.001292 Article
  13. Wu, Z.; Tiambeng, T. N.; Cai, W.; Chen, B.; Lin, Z.; Gregorich, Z. R.; Ge, Y., Impact of phosphorylation on the mass spectrometry quantification of intact phosphoproteins, Anal. Chem., 2018, 90, 8, 4935-4939, DOI:10.1021/acs.analchem.7b05246 Article
  14. Gao, L.; Gregorich, Z. R.; Zhu, W.; Mattapally, S.; Lou, X.; Borovjagin, A. V.; Walcott, G. P.; Pollard, A. E.; Fast, V. G.; Ge, Y.; Zhang, J. Large cardiac-muscle patches engineered from human induced-pluripotent stem-cell–derived cardiac cells improve recovery from myocardial infarction in swine, Circulation, 2018, 137, 16, 1712-1730, DOI:10.1161/CIRCULATIONAHA.117.030785 Article
  15. Smelter, D. F., De Lange, W. J., Cai, W., Ge, Y., Ralphe, J. C., The HCM-linked W792R mutation in cardiac myosin binding protein-C reduces C6 FnIII domain stability. Am J Physiol Heart Circ Physiol. 2018, 314, 6, H1179-H1191. DOI: 10.1152/ajpheart.00686.2017. Article
  16. Lin, Z.; Guo, F.; Gregorich, Z. R.; Sun, R.; Zhang, H.; Hu, Y.; Shanmuganayagam, D.; Ge, Y., Comprehensive characterization of swine cardiac troponin T proteoforms by top-down mass spectrometry, J. Am. Soc. Mass Spectrom. 2018, Accepted.
  17. Lam, M. P. Y.; Ge, Y., Harnessing the power of proteomics to assess drug safety and guide clinical trials, Circulation, 2018, 137, 1011-1014.
  18. Aebersold, R.; Agar, J. N.; Amster, I. J.; Baker, M. S.; Bertozzi, C. R.; Boja, E. S.; Costello, C. E.; Cravatt, B. F.; Fenselau, C.; Garcia, B. A.; Ge, Y.; Gunawardena, J.; Hendrickson, R. C.; Hergenrother, P. J.; Huber, C. G.; Ivanov, A. R.; Jensen, O. N.; Jewett, M. C.; Kelleher, N. L.; Kiessling, L. L.; Krogan, N. J.; Larsen, M. R.; Loo, J. A.; Ogorzalek Loo, R. R.; Lundberg, E.; MacCoss, M. J.; Mallick, P.; Mootha, V. K.; Mrksich, M.; Muir, T. W.; Patrie, S. M.; Pesavento, J. J.; Pitteri, S. J.; Rodriguez, H.; Saghatelian, A.; Sandoval, W.; Schlüter, H.; Sechi, S.; Slavoff, S. A.; Smith, L. M.; Snyder, M. P.; Thomas, P. M.; Uhlén, M.; Van Eyk, J. E.; Vidal, M.; Walt, D. R.; White, F. M.; Williams, E. R.; Wohlschlager, T.; Wysocki, V. H.; Yates, N. A.; Young, N. L.; Zhang, B., How many human proteoforms are there? Nat. Chem. Biol. 2018, 14, 206-214. doi: 10.1038/nchembio.2576.
  19. LeDuc, R.D.; Schwämmle, V.; Shortreed, M.R.; Cesnik, A.J.; Solntsev, S.K.; Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge, Y., Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO. ProForma: A Standard Proteoform Notation. J. Proteome Res. 2018, 17, 1321-1325. doi: 10.1021/acs.jproteome.7b00851.
  20. Chen, Z., Song, J., Chen, L., Zhu, C., Cai, H., Sun, M., Stern, A., Mozdziak, P., Ge, Y., Means, W. J., Guo, W., Characterization of TTN Novex Splicing Variants across Species and the Role of RBM20 in Novex-Specific Exon Splicing. Genes, 2018, 9, 86. DOI: 10.3390/genes9020086
  21. Seok, S.H.; Ma, Z.X.; Feltenberger, J. B.; Chen, H.; Chen, H.; Scarlett, C.; Lin, Z.; Satyshur, K.A.; Cortopassi, M.; Jefcoate, C.R.; Ge, Y.; Tang, W.; Bradfield, C. A.; Xing, Y. Trace derivatives of kynurenine potently activate the aryl hydrocarbon receptor (AHR). J Biol Chem. 2018, 293, 1994-2005. DOI: 10.1074/jbc.RA117.000631
  22. Chen, B.; Brown, K.A.; Lin, Z.; Ge, Y. Top-down proteomics: ready for prime time? Anal. Chem., 2018, 90, 1, 110-127, DOI: 10.1021/acs.analchem.7b04747.
  23. Wei, L.; Gregorich, Z. R.; Lin, Z.; Cai, W.; Jin, Y.; McKiernan, S. H.; Mcilwain, S.; Aiken, J. M.; Moss, R. L.; Diffee, G. M.; Ge, Y. Novel sarcopenia-related alterations in sarcomeric protein post-translational modifications in skeletal muscles identified by top-down proteomics, Mol. Cell. Proteomics, 2018, 17, 134-145, DOI: 10.1074/mcp.RA117.000124
  24. Hu, C.; Worth, M.; Fan, D.; Li, B.; Li, H.; Lu, L. Zhong, X.; Lin, Z.; Wei, L.; Ge, Y.; Li, L.; Jiang, J. Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase, Nat. Chem. Biol., 2017, 13, 1267-1273. DOI: 10.1038/nchembio.2494.
  25. Rana, A. S. J. B.; Ge, Y.; Strieter, E. R. Ubiquitin chain enrichment middle-down mass spectrometry (ubichem-ms) reveals cell-cycle dependent formation of lys11/lys48 branched ubiquitin chains. J. Proteome Res., 2017, 16, 3363-3369. DOI: 10.1021/acs.jproteome.7b00381.
  26. Chen, B.; Guo, X.; Tucholski, T.; Lin, Z.; Mcilwain, S.; Ge, Y. The impact of phosphorylation on electron capture dissociation of proteins: a top-down perspective. J. Am. Soc. Mass Spectrom., 2017, 28, 1805–1814. DOI: 10.1007/s13361-017-1710-3
  27. Wu, C.-G., Chen, H., Guo, F., Yadav, V. K., McIlwain, S. J., Rowse, M., Choudhary, A., Lin, Z., Li, Y., Gu, T., Zheng, A., Xu, Q., Lee, W., Resch, E., Johnson, B., Day, J., Ge, Y., Ong, I. M., Burkard, M. E., Ivarsson, Y., Xing, Y. PP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis. Cell Disc. 2017, 3, 17027. DOI:10.1038/celldisc.2017.27
  28. Gregorich Z. R.; Cai, W.; Lin, Z.; Chen, A. J.; Peng, Y.; Kohmoto, T.; Ge, Y. Distinct sequences and post-translational modifications in cardiac atrial and ventricular myosin light chains revealed by top-down mass spectrometry. J. Mol. Cell. Cardiol., 2017, 107, 13-21. DOI: 10.1016/j.yjmcc.2017.04.002.
  29. Cai, W.; Tucholski, T.; Chen, B.; Alpert, A. J.; McIlwain, S.; Kohmoto, T.; Jin, S.; Ge, Y. Top–down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Anal Chem., 2017, 89, 5467-5475. DOI: 10.1021/acs.analchem.7b00380.
  30. Jin, Y.; Wei, L.; Cai, W.; Lin, Z.; Wu, Z.; Peng, Y.; Kohmoto, T.; Moss, R. M.; Ge, Y. Complete Characterization of Cardiac Myosin Heavy Chain (223 kDa) Enabled by Size-Exclusion Chromatography and Middle-down Mass Spectrometry. Anal Chem., 2017, 89, 4922-4930. DOI: 10.1021/acs.analchem.7b00113.
  31. Chen, B.; Hwang, L.; Ochowicz, W.; Lin, Z.; Guardado-Alvarez, T. M.; Cai, W.; Xiu, L.; Dani, K.; Colah, C.; Jin, S.; Ge, Y. Coupling Functionalized Cobalt Ferrite Nanoparticle Enrichment with Online LC/MS/MS for Top-down Phosphoproteomics. Chem. Sci., 2017, DOI: 10.1039/C6SC05435H.
  32. Yang, L; Gregorich Z. R.; Cai, W.; Zhang, P; Young, B; Gu, Y; Zhang, J; Ge, Y. Quantitative Proteomics and Immunohistochemistry Reveal Insights into Cellular and Molecular Processes in the Infarct Border Zone One Month after Myocardial Infarction. J. Proteome Res., 2017, 16, 2101-2112. DOI: 10.1021/acs.jproteome.7b00107.
  33. Crowe, S. O.; Rana, A. S.; Deol, K. K.; Ge, Y.; Strieter, E. R. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in Cellulo. Anal Chem., 2017, 89, 4428-4434. DOI: 10.1021/acs.analchem.6b03675.
  34. Gregorich Z. R.; Cai, W.; Jin, Y.; Wei, L.; Chen, A. J.; McKiernane, S. H.; Aiken, J. M.; Moss, R. L.; Diffee, G. M.; Ge, Y. Top-down targeted proteomics reveals decrease in myosin regulatory light chain phosphorylation that contributes to sarcopenic muscle dysfunction. J. Proteome Res., 2016, 15 (8), pp 2706–2716. DOI: 10.1021/acs.jproteome.6b00244.

     More publications