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

Professor, Department of Cell and Regenerative Biology
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

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    News and Updates

  • July 2019, MASH Explorer software is available to the public. You can download the software using this link. [Link]
  • June 2019, Dr. Bifan Chen and Dr. Yutong Jin have left our research group. Bifan will be joining Genentech and Yutong will be working for Biogen. They will for sure be missed by our lab members! [Photos]
  • June 2019, The Ge Group attended the 2019 ASMS Conference in Atlanta, GA! [Photos]
  • May 2019, The Ge Group celebrated Dr. Bifan Chen's and Dr. Yuton Jin's graduation! Congratulations to you both! [Photos]
  • May 2019, Follow us on Twitter at @Ge_Lab_UW!
  • 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]

Most Recent Publications

  1. Cai, W.; Zhang, J.; De Lange, W. J.; Gregorich, Z. R.; Karp, H.; Ferrell, E. T.; Mitchell, S. T.; Tucholski, T.; Lin, Z.; Biermann, M.; McIlwain, S.; Ralphe, J. C.; Kamp, T. J.; Ge, Y. Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes., Circ Res., in press Article.
  2. Tiambeng, T. N.; Tucholski, T.; Wu, Z.; Zhu, Y.; Mitchell, S. D.; Roberts, D. S.; Jin, Y.; Ge, Y. Analysis of cardiac troponin proteoforms by top-down mass spectrometry, Methods Enzymol., ISSN 0076-6879 Article.
  3. Wu, Z.; Jin, Y.; Chen, B.; Gugger, M. K.; Wilkinson-Johnson, C. L.; Tiambeng, T. N.; Jin, S.; Ge, Y., Comprehensive Characterization of Recombinant Catalytic Subunit of cAMP-Dependent Protein Kinase by Top-Down Mass Spectrometry, J. Am. Soc. Mass Spectrom., accepted.
  4. Smith, L. M.; Thomas, P. M.; Shortreed, M. R.; Scheffer, L. V.; Fellers, R. T.; LuDec, R. D.; Tucholski, T.; Ge, Y.; Agar, J. N.; Anderson, L. C.; Chamot-Rooke, J.; Gault, J.; Loo, J. A.; Pasa-Tolic, L.; Robinson, C. V.; Schluter, H.; Tsybin, Y. O.; Vilaseca, M.; Vizcaino, J. A.; Danis, P. O.; Kelleher, N. L., A five-level classification system for proteoform identifications, Nature Methods. 2019, 16, 939-940. Article.
  5. Chen, B.; Lin, Z.; Zhu, Y.; Jin, Y.; Larson, E.; Xu, Q.; Fu, C.; Zhang, Z.; Zhang, Q.; Pritts, W. A.; Ge, Y. Middle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation., Anal Chem. 2019, 16, 18, 11661-11669. Article.
  6. Schaffer, L. A.; Tucholski, T.; Shortreed, M. R.; Ge, Y.; Smith, L. M., Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms., Anal Chem. 2019, 19, 10937-10942. Article.
  7. Biermann, M.; Cai, W.; Lang, D.; Hermsen, J.; Profio, L.; Zhou, Y.; Czirok, A.; Isai, D. G.; Napiwocki, B. N.; Rodriguez, A. M.; Brown, M. E.; Woon, M. T.; Shao, A.; Han, T.; Park, D.; Hacker, T. A.; Crone, W. C.; Burlingham, W. J.; Glukhov, A. V.; Ge, Y.; Kamp, T. J., Epigenetic Priming of Human Pluripotent Stem Cell-Derived Cardiac Progenitor Cells Accelerates Cardiomyocyte Maturation, Stem Cells. 2019, 37, 910-923. Article.
  8. 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, 16, 417-420. News Release.
  9. Donnelly, D. P.; Rawlins, C. M.; DeHart, C. J.; Fornelli,, L.; Schachner, L. F.; Lin, Z.; Lippens, J. L.; Aluri, K. C.; Sarin, R.; Chen, B.; Lantz, C.; Jung, W.; Johnson, K. R.; Koller, A.; Wolff, J. J.; Campuzano, I. D. G.; Auclair, J. R.; Ivanov, A. R.; Whitelegge, J. P.; Paša-Tolić, L.; Chamot-Rooke, J.; Danis, P. O.; Smith, L. M.; Tsybin, Y. O.; Loo, J. A.; Ge Y.; Kelleher N. L.; Agar J. N. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry., Nature Methods. 2019, 16, 587-594. Article.
  10. Schaffer, L. V.; Millikin, R. J.; Miller, R. M.; Anderson, L. C.; Fellers R. T.; Ge Y.; Kelleher N. L.; LeDuc R. D.; Liu X.; Payne, S. H.; Sun, L.; Thomas, P. M.; Tucholski, T.; Wang, Z.; Wu, S.; Wu, Z.; Yu, D.; Shortreed, M. R.; Smith, L. M. Identification and Quantification of Proteoforms by Mass Spectrometry, Proteomics, 2019, 19, 1800361 Article.
  11. Roberts, D. S.; Chen, B.; Tiambeng, T. N.; Wu, Z.; Ge, Y.; Jin, S. Reproducible large-scale synthesis of surface silanized nanoparticles as an enabling nanoproteomics platform: Enrichment of the human heart phosphoproteome, Nano Res., 2019, 12, 1473-1481. DOI: 10.1007/s12274-019-2418-4. Article.
  12. 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
  13. 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
  14. 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
  15. 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

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