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.

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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

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

  • December 2024, Bella Clemmer, Kwame Osei, and Thomas Weir joined our lab from the Chemistry program! Welcome to the Ge Group!
  • December 2024, Kalina Rossler and her husband welcomed their first daughter into their family. We're so thankful for the Ge lab's litlest mass spectrometrist!
  • October 2024, Congratulations to Ruby for receiving an ASMS travel award to attend the Native MS Fall workshop!
  • September 2024, Congratulations to Ying for being named a Top 10 Human Health Hero on the 2024 Analytical Scientist Power List!
  • August 2024, Dr. Timothy Aballo successfully defended his thesis and is now a member of the AbbVie team. Hold onto your hat in the windy city!
  • July 2024, Dr. Melissa Pergande has rolled over to a tenure-track position at Boston University. We'll miss you, big dog!
  • May 2024, longtime undergraduate research assistant Brad Li graduated and is headed to Vanderbilt University School of Medicine! Congratulations and good luck!
  • May 2024, Dr. Benjamin Wancewicz successfully defended his thesis. We're excited to see you fly high!
  • May 2024, Registration and Abstract submission is now open for the Wisconsin Human Proteomics Symposium to be held in Madison, WI, July 31 - Aug. 1, 2024. Register and submit your abstract here: [Link]
  • April 2024, Mallory Wilson was awarded the highly competitive NSF GRFP! Congratulations!
  • April 2024, Congratulations to Matthew Fischer and Andrew Perciaccante for being awarded highly competitive Honorable Mentions by the NSF GRFP!
  • March 2024, Congratulations to alumni Dr. David S. Roberts for winning an ASMS Postdoctoral Career Development Award, Emily Chapman for receiving an ASMS Graduate Student Award, and Brad Li for receiving an ASMS Undergraduate Student Award! A clean sweep for the Ge Group!
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Most Recent Publications

  1. Chan, H.-J.; Krichel, B.; Bandura, L. J.; Chapman, E. A.; Rogers, H. T.; Fischer, M. S.; Roberts, D. S.; Gao, Z.; Wang, M.-D.; Wu, J.; Uetrecht, C.; Jin, S.; Ge, Y. Structural Heterogeneity of Proteoform-Ligand Complexes in AMP-Activated Protein Kinase Uncovered by Integrated Top-Down Mass Spectrometry. bioRxiv 2025, doi: https://doi.org/10.1101/2025.04.15.648965
  2. Fischer, M. S.; Rogers, H. T.; Chapman, E. A.; Jin, S.; Ge, Y., Native Top-Down Proteomics of Endogenous Protein Complexes Enabled by Online Two-Dimensional Liquid Chromatography. bioRxiv 2025, 2025.03. 28.645965. doi: https://doi.org/10.1101/2025.03.28.645965
  3. Liu, M.; Zhu, Y.; McIlwain, S. J.; Deng, H.; Brasier, A. R.; Ge, Y.; Kimple, M. E.; Baschnagel, A. M., Characterizing Plasma-based Metabolomic Signatures for Metastasis in Non-Small Cell Lung Cancer. 2025.
  4. Liu, X.; Roberts, D. S.; Bingman, C. A.; Jin, S.; Ge, Y.; Gellman, S. H., Rational design of a foldon-derived heterotrimer guided by quantitative native mass spectrometry. bioRxiv 2025, 2025.03. 25.645370.
  5. Aballo, T. J.; Bae, J.; Paltzer, W. G.; Chapman, E. A.; Perciaccante, A. J.; Pergande, M. R.; Salamon, R. J.; Nuttall, D. J.; Mann, M. W.; Ge, Y., Integrated Proteomics identifies troponin I isoform switch as a Regulator of a Sarcomere-Metabolism Axis during Cardiac Regeneration. Cardiovasc. Res. 2025, cvaf069. Article
  6. Towler, A. G.; Perciaccante, A. J.; Aballo, T. J.; Zhu, Y.; Wang, F.; Lloyd, S.; Kadoya, K.; He, Y.; Tian, Y.; Ge, Y., A Single-Step Protein Extraction for Lung Extracellular Matrix Proteomics Enabled by the Photocleavable Surfactant Azo and timsTOF Pro. Mol. Cell.Proteomics 2025, 100950. Article
  7. Reasoner, E. A.; Chan, H.-J.; Aballo, T. J.; Plouff, K. J.; Noh, S.; Ge, Y.; Jin, S., In Situ Metal–Organic Framework Growth in Serum Encapsulates and Depletes Abundant Proteins for Integrated Plasma Proteomics. ACS nano 2025, 19, 13968–13981. Article
  8. Knott, S. J.; Tucholski, T.; Josyer, H.; Inman, D.; Friedl, A.; Zhu, Y.;; Ge Y.; Ponik, S. M., Deciphering Proteoform Landscape of Mammary Carcinoma by Top-Down Proteomics. J. Proteome Res. 2025, 24, 3, 1425–1438. Article
  9. Chapman, E. A.; Rogers, H. T.; Gao, Z.; Chan, H.-J.; Alvarado, F. J.; Ge, Y., In-depth characterization of S-glutathionylation in ventricular myosin light chain 1 across species by top-down proteomics. J. Mol. Cell. Cardiol. 2025. doi: 10.1016/j.yjmcc.2025.03.012. Online ahead of print. Article
  10. Gregorich, Z.R.; Larson, E.J.; Zhang, Y.; Braz, C.U.; Ge, Y.; Guo, W., Integrated proteomics and transcriptomics analysis reveals insights into differences in premature mortality associated with disparate pathogenic RBM20 variants. J. Mol. Cell. Cardiol., 2024, 197, 78-89. Article
  11. Turner, D.G.P.; De Lange, W. J.; Zhu, Y.; Coe, C.L.; Simcox, J.; Ge, Y.; Kamp, T.J.; Ralphe, J.C.; Glukhov, A.V., Neutral sphingomyelinase regulates mechanotransduction in human engineered cardiac tissues and mouse hearts. J. Physiol., 2024, 602 (18), 4387-4407 Article
  12. Fischer, M.S.; Rogers, H.T.; Chapman, E.A.; Chan, H.; Krichel, B.; Gao, Z.; Larson, E.J.; Ge, Y., Online Mixed-Bed Ion Exchange Chromatography for Native Top-Down Proteomics of Complex Mixtures. J. Proteome Res., 2024, 23 (7), 2315-2322. Article
  13. Roberts, D. S.; Loo, J. A.; Tsybin, Y. O.; Liu, X.; Wu, S.; Chamot-Rooke, J.; Agar, J. N.; Paša-Tolić, L.; Smith, L. M.; Ge, Y., Top-down proteomics. Nature Reviews Methods Primers 2024, 4 (1), 38. Article
  14. Wang, Y.; Zhao, M.; Liu, X.; Xu, B.; Reddy, G. R.; Jovanovic, A.; Wang, Q.; Zhu, C.; Xu, H.; Bayne, E. F.; Xiang, W.; Tilley, D. G.; Ge, Y.; Tate, C. G.; Feil, R.; Chiu, J. C.; Bers, D. M.; Xiang, Y. K., Carvedilol Activates a Myofilament Signaling Circuitry to Restore Cardiac Contractility in Heart Failure. JACC: Basic to Translational Science 2024. Article
  15. Habeck, T.; Brown, K. A.; Des Soye, B.; Lantz, C.; Zhou, M.; Alam, N.; Hossain, M. A.; Jung, W.; Keener, J. E.; Volny, M.; Wilson, J. W.; Ying, Y.; Agar, J. N.; Danis, P. O.; Ge, Y.; Kelleher, N. L.; Li, H.; Loo, J. A.; Marty, M. T.; Paša-Tolić, L.; Sandoval, W.; Lermyte, F., Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nature Methods 2024. Article
  16. Stroik, D.; Gregorich, Z. R.; Raza, F.; Ge, Y.; Guo, W., Titin: roles in cardiac function and diseases. Front Physiol 2024, 15, 1385821. Article
  17. Anderson, C. L.; Brown, K. A.; North, R. J.; Walters, J. K.; Kaska, S. T.; Wolff, M. R.; Kamp, T. J.; Ge, Y.; Eckhardt, L. L., Global Proteomic Analysis Reveals Alterations in Differentially Expressed Proteins between Cardiopathic Lamin A/C Mutations. Journal of Proteome Research 2024,23 (6), 1970-1982. Article
  18. Wancewicz, B.; Pergande, M. R.; Zhu, Y.; Gao, Z.; Shi, Z.; Plouff, K.; Ge, Y., Comprehensive Metabolomic Analysis of Human Heart Tissue Enabled by Parallel Metabolite Extraction and High-Resolution Mass Spectrometry. Anal Chem 2024,96 (15), 5781-5789. Article
  19. Rossler, K. J.; de Lange, W. J.; Mann, M. W.; Aballo, T. J.; Melby, J. A.; Zhang, J.; Kim, G.; Bayne, E. F.; Zhu, Y.; Farrell, E. T.; Kamp, T. J.; Ralphe, J. C.; Ge, Y., Lactate- and immunomagnetic-purified hiPSC-derived cardiomyocytes generate comparable engineered cardiac tissue constructs. JCI Insight, 2024, Article
  20. Chapman, E. A.; Li, B. H.; Krichel, B.; Chan, H.-J.; Buck, K. M.; Roberts, D. S.; Ge, Y. Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate. J. Am. Soc. Spectr. 2024, Article
  21. Bayne, E. F.; Buck, K. M.; Tower, A. G.; Zhu, Y.; Pergande, M. R.; Zhou, T.; Price, S.; Rossler, K. J.; Morales-Tirado, V.; Lloyd, S.; Wang, F.; He, Y.; Tian, Y.; Ge, Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024, Article
  22. Paltzer, W. G.; Aballo, T. J.; Bae, J.; Flynn, C. G. K.; Wanless, K. N.; Hubert, K. A.; Nuttall, D. J.; Perry, C.; Malawi, R.; Ge, Y.; Mahmoud, A. I., mTORC1 regulates the metabolic switch of postnatal cardiomyocytes during regeneration. J. Mol. Cell. Cardiol. 2024 Article
  23. Rogers, H. T.; Melby, J. A.; Ehlers, L. E.; Fischer, M. S.; Larson, E. J.; Gao, Z.; Rossler, K. J.; Wang, D.; Alpert, A. J.; Ge, Y. Small-Scale Serial Size Exclusion Chromatography (s3SEC) for High Sensitivity Top-Down Proteomics of Large Proteoforms. Anal. Chem. 2024 Article
  24. Chapman, E. A.; Roberts, D. S.; Tiambeng, T. N.; Andrews, J.; Wang, M.-D.; Reasoner, E. A.; Melby, J. A.; Li, B. H.; Kim, D.; Alpert, A. J.; Jin, S.; Ge, Y. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nature Communications 2023, 14, 8400. Article
  25. Brown, K. A.; Morris, R. K.; Eckhardt, S. J.; Ge, Y.; Gellman, S. H. Phosphorylation Sites of the Gastric Inhibitory Polypeptide Receptor (GIPR) Revealed by Trapped-Ion-Mobility Spectrometry Coupled to Time-of-Flight Mass Spectrometry (TIMS-TOF MS). J. Am. Chem. Soc. 2023, Epub ahead of Print Article
  26. West, K. H. J.; Ma, S. V.; Pensinger, D. A.; Tucholski, T.; Tiambeng, T. N.; Eisenbraun, E. L.; Yehuda, A.; Hayouka, Z.; Ge, Y.; Sauer, J.; Blackwell, H. E. Characterization of an Autoinducing Peptide Signal Reveals Highly Efficacious Synthetic Inhibitors and Activators of Quorum Sensing and Biofilm Formation in Listeria monocytogenes. Biochemistry. 2023. Article
  27. Lermyte, F.; Habeck, T.; Brown, K.; Des Soye, B.; Lantz, C.; Zhou, M.; Alam, N.; Hossain, M.A.; Jung, W.; Keener, J.; Volny, M.; Wilson, J.; Ying, Y.; Agar, J.; Danis, P.; Ge, Y.; Kelleher, N.; Li, H.; Loo, J.; Marty, M.; Pasa-Tolic, L.; Sandoval, W. Top-down mass spectrometry of native proteoforms and their complexes: A community study. Under review at Nature Portfolio. 2023. PREPRINT
  28. Wancewicz, B.; Zhu, Y.; Fenske, R.J.; Weeks, A.M.; Wenger, K.; Pabich, S.; Daniels, M.; Punt, M.; Nall, R.; Peter, D.C.; Brasier, A.; Cox, E.D.; Davis, D.B.; Ge, Y.; Kimple, M.E. Metformin monotherapy alters the human plasma lipidome independent of clinical markers of glycemic control and cardiovascular disease risk in a type 2 diabetes clinical cohort. Journal of Pharmacology and Experimental Therapeutics. 2023. Article
  29. Yan, J.; Wu, Q.; Maity, M.; Braun, D.R.; Alas, I.; Wang, X.; Ying, X.; Zhu, Y.; Bell, B.A.; Rajski, S.R.; Ge, Y.; Richardson, D.D.; Zhong, W.; Bugni, T.S. Rapid Unambiguous Structure Elucidation of Streptnatamide A, a New Cyclic Peptide Isolated from A Marine-derived Streptomyces sp. Chemistry -A European Journal. 2023. Article
  30. Pergande, M. R.; Osterbauer, K. J.; Buck, K. M.; Roberts, D. S.; Wood, N. N.; Balasubramanian, P.; Mann, M. W.; Rossler, K. J.; Diffee, G. M.; Colman, R. J.; Anderson, R. M.; Ge, Y. Mass Spectrometry-Based Multiomics Identifies Metabolic Signatures of Sarcopenia in Rhesus Monkey Skeletal Muscle. Journal of Proteome Research 2023.Article
  31. Melby, J.A.; Brown, K.A.; Gregorich, Z.R.; Roberts, D.S.; Chapman, E.A.; Ehlers, L.E.; Gao, Z.; Larson, E.J.; Jin, Y.; Lopez, J.R.; Hartung, J.; Zhu, Y.; McIlwain, S.J.; Wang, D.; Guo, W.; Diffee, G.M.; Ge, Y. High sensitivity top-down proteomics captures single muscle cell heterogeneity in large proteoforms. PNAS. 2023, 120(19), e2222081120. Article
  32. Rossler, K.J.; de Lange, W.; Mann, M.W.; Aballo, T.J.; Melby, J.A.; Zhang, J.; Kim, G.; Bayne, E.F.; Zhu, Y.; Farrell, E.T.; Kamp, T.J.; Ralphe, J.C.; Ge, Y. Lactate and Immunomagnetic-purified iPSC-derived Cardiomyocytes Generate Comparable Engineered Cardiac Tissue Constructs. JCI Insight. 2023. Article
  33. Rogers, H.T.; Roberts, D.S.; Larson, E.J.; Melby, J.A.; Rossler, K.J.; Carr, A.V.; Brown, K.A.; Ge, Y. Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics. Anal. Chem. 2023. Article
  34. Wancewicz, B.; Zhu, Y.; Fenske, R.K.; Weeks, A.M.; Wenger, K.; Pabich, S.; Daniels, M.; Punt, M.; Nall, R.; Peter, D.C.; Brasier, A.; Cox, E.D.; Davis, D.B.; Ge, Y.; Kimple, M. Metformin Monotherapy Alters the Human Plasma Lipidome Independent of Clinical Markers of Glycemic Control and Cardiovascular Disease Risk in a Type 2 Diabetes Clinical Cohort. J. of Pharmacology and Exp. Therapeutics. 2023. Article
  35. Aballo, T. J.; Roberts, D.S.; Bayne, E. F.; Zhu, W.; Walcott, G.; Mahmoud, A. I.; Zhang, J.; Ge, Y. Integrated Proteomics Reveals Alterations in Sarcomere Composition and Developmental Processes during Postnatal Swine Heart Development, J. Mol. Cell. Cardiol. 2023, 176, 33-40 Article
  36. Larson, E.J. ; Pergande, M. R; Moss, M. E.; Rossler, K. J.; Wenger, R. K.; Krichel, B.; Josyer, H.; Melby, J. A.; Roberts, D. S.; Pike, K.; Shi, Z.; Chan, H.; Knight, B.; Rogers, H. T.; Brown, K. A.; Ong, I. M.; Kyowon Jeong, K.; Marty, M.; McIlwain, S. J.; Ge, Y. MASH Native: A Unified Solution for Native Top-Down Proteomics Data Processing Bioinformatics 2023, btad359 Article
  37. Mann, M.; Fu, Y.; Xu, X.; Roberts, D.S.; Li, Y.; Zhou, J., Ge, Y.; Brasier, A.R. Bromodomain-containing Protein 4 Regulates Innate Inflammation in Airway Epithelial Cells via Modulation of Alternative Splicing. Front. Immunol., 2023, 14, Article
  38. Chapman, E.; Aballo, J. J.; Melby, J.A.; Zhou, T.; Price, S. J.; Rossler, K. J.; Lei, I.; Tang, P. C.; Ge, Y. Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-down Proteomics, J. Proteome Res. 2023, 22, 931-941 Article
  39. Bayne, E.F.; Rossler, K. J.; Gregorich, Z. R.; Aballo, T. J.; Roberts, D.S.; Chapman, E. A.;Guo, W.; Ralphe, J.C.; Kamp, T.J.; Ge, Y. Top-down Proteomics of Myosin Light Chain Isoforms Define Chamber-Specific Expression in the Human Heart, J Mol Cell Cardiol 2023, 181, 89-97. Article
  40. Brown, K. A.; Gugger, M. K.; Roberts, D. S.; Moreno, M.; Chae, P. S.; Ge, Y.; Jin, S. Synthesis, Self-Assembly Properties, and Degradation Characterization of a Nonionic Photocleavable Azo-Sulfide Surfactant Family, Langmuir, 2023, DOI: 10.1021/acs.langmuir.2c02820 Article
  41. Wu, Q.; Bell, B.A.; Yan, J.; Chevrette, M.G.; Brittin, N.J.; Zhu, Y.; Chanana, S.; Maity, M.; Braun, D.R.; Wheaton, A.M.; Guzei, I.A.; Ge, Y.; Rajski, S.R.; Thomas, M.G.; Bugni, T.S.; SR Metabolomics and Genomics Enable the Discovery of a New Class of Nonribosomal Peptidic Metallophores from a Marine Micromonospora. J. Am. Chem. Soc. 2023, 145, 58–69. Article
  42. Brown, K.A.; Gugger, M.; Yu, Z.; Moreno, D.; Jin, S.; Ge, Y. A Nonionic, Cleavable Surfactant for Native Mass Spectrometry and Top-down Proteomics, Anal. Chem. 2023, 95, 1801–1804 Article
  43. Wu, Q.; Bell, B.A.; Yan, J.; Chevrette, M.G.; Brittin, N.J.; Zhu, Y.; Chanana, S.; Maity, M.; Braun, D.R.; Wheaton, A.M.; Guzei, I.A.; Ge, Y.; Rajski, S.R.; Thomas, M.G.; Bugni, T.S.; SR Metabolomics and Genomics Enable the Discovery of a New Class of Nonribosomal Peptidic Metallophores from a Marine Micromonospora. J. Am. Chem. Soc., 2023, 145, 58–69.Article
  44. Sun M.; Jin Y.; Zhang Y.; Gregorich Z.R.; Ren J.; Ge Y.; Guo W.; SR Protein Kinases Regulate the Splicing of Cardiomyopathy-Relevant Genes via Phosphorylation of the RSRSP Stretch in RBM20. Genes, 2022, 13(9), 1526. Article.
  45. Roberts, D.S.; Mann, M.; Li, B.H.; Kim, D.; Brasier, A.R.; Jin, S. Ge, Y. Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry. Chem. Sci. 2022, 13, 10944-10949. Article.
  46. Larson, E.J.; Gregorich, Z.R.; Zhang, Y.; Li, B.H.; Aballo, T.J.; Melby, J.A.; Ge, Y.; Guo, W. RBM20 Ablation is Associated With Changes in The Expression of Titin-Interacting and Metabolic Proteins. Molecular Omics, 2022. Article.
  47. Gupta, K.; Brown, K.A.; Hsieh, M.L.; Hoover, B.; Wang, J.; Khoury, M.K.; Pilli, V.S.S.; Beyer, R.S.; Voruganti, N.R.; Chaudhary, S.; Roberts, D.S.; Murphy, R.M.; Hong, S.; Ge, Y.; Liu, B. Necroptosis is associated with Rab27-independent expulsion of extracellular vesicles containing RIPK3 and MLKL. Journal of Extracellular Vesicles, 2022, 11, e12261. Article.
  48. Zhu, Y.; Esnault, S.; Ge, Y.; Jarjour, N.N; Brasier, A.R. Airway fibrin formation cascade in allergic asthma exacerbation: implications for inflammation and remodeling. Clin Proteomics. 2022, 19(1), 15. Article.
  49. Zhu, Y.; Esnault, S.; Ge, Y.; Jarjour, N.N.; Brasier, A.R. Segmental Bronchial Allergen Challenge Elicits Distinct Metabolic Phenotypes in Allergic Asthma. Metabolites, 2022, 12(5), 381. Article.
  50. Tiambeng, T.N.; Wu, Z.; Melby, J.A.; Ge, Y. Size Exclusion Chromatography Strategies and MASH Explorer for Large Proteoform Characterization. Methods Mol Biol. 2022, 2500, 15-30. Article.
  51. Zhang, Y.; Wang, C.; Sun, M.; Jin, Y.; Braz, C.U.; Khatib, H.; Hacker, T.A.; Liss, M.; Gotthardt, M.; Granzier, H.; Ge, Y.; Guo, W. RBM20 phosphorylation and its role in nucleocytoplasmic transport and cardiac pathogenesis. FASEB Journal, 2022, Epub ahead of print. Article.
  52. Buck, K.M.; Roberts, D.S.; Aballo, T.J.; Inman, D.R.; Jin, S.; Ponik, S.; Brown, K.A.; Ge, Y. One-Pot Exosome Proteomics Enabled by a Photocleavable Surfactant. Anal. Chem., 2022, 94, 7164-7168. Article.
  53. Li, A.; Campbell, K.; Lal, S.; Ge, Y.; Keogh, A.; Macdonald, P.S.; Lau, P.; Linke, W.A.; Van der Velden, J.; Field, A.; Martinac, B.; Grosser, M.; dos Remedios, C. Peripartum cardiomyopathy: a global effort to find the cause and cure for the rare and little understood disease Biophysical Reviews. 2022, 14, 369-379. Article.

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