Publications

At UW-Madison:

    2019

  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. Article. 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
  16. 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
  17. 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

  18. 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
  19. 2018

  20. 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
  21. 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

  22. 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

  23. 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
  24. 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

  25. 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

  26. 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
  27. 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.
  28. Lam, M. P. Y.; Ge, Y., Harnessing the power of proteomics to assess drug safety and guide clinical trials, Circulation, 2018, 137, 1011-1014. Article

  29. 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. Article
  30. 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. Article

  31. 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 Article
  32. 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 Article
  33. 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. Article

  34. 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 Article

  35. 2017

  36. 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. Article
  37. 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. Article

  38. 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 Article

  39. 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 Article

  40. 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. Article

  41. 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. Article

  42. 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. Article

  43. 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. Article

  44. 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. Article

  45. 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. Article

  46. 2016

  47. 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. Article

  48. Crowe, S.O.; Pham, G.H.; Ziegler, J.C.; Deol, K.K.; Guenette, R.G.; Ge, Y.; Strieter, E.R. Subunit-specific labeling of ubiquitin chains by using sortase: insights into the selectivity of deubiquitinases. ChemBioChem., 2016, 17(16):1525-31. DOI: 10.1002/cbic.201600276. Article
  49. Cai, W.; Tucholski, T. M.; Gregorich Z. R.; Ge, Y. Top-down proteomics: technology advancements and application to heart diseases. Expert Rev. Proteomics., 2016, 13, 717-730. DOI: 10.1080/14789450.2016.1209414 Article

  50. Jin, Y.; Peng, Y.; Lin, Z.; Chen, Y. C.; Wei, L.; Hacker, T. A.; Larsson, L.; Ge, Y. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. J Muscle Res Cell Motil., 2016, 37(1-2):41-52. DOI: 10.1007/s10974-016-9443-7. Article
  51. Hwang, L.; Guardado-Alvarez†, T.; Ayaz-Gunner, S.; Ge, Y.; Jin S. A Family of Photolabile Nitroveratryl-Based Surfactants That Self-Assemble into Photodegradable Supramolecular Structures. Langmuir, 2016, 32 (16): pp 3963–3969. Article

  52. Chen, B.; Peng, Y.; Valeja, S. G.; Xiu, L.; Alpert, A. J.; Ge, Y. Online Hydrophobic Interaction Chromatography-Mass spectrometry for Top-down Proteomics. Anal. Chem. 2016, 88(3):1885-91. Article

  53. Cai, W.; Guner, H.; Gregorich, Z. R.; Chen, A. J.; Ayaz-Guner, S.; Peng, Y.; Valeja, S. G.; Liu, X.; Ge, Y. MASH Suite Pro: A Comprehensive Software Tool for Top-down Proteomics. Mol. Cell. Proteomics. 2016, 15(2):703-14. Article

  54. Yu, D.; Peng, Y.; Ayaz-Guner, S.; Gregorich Z. R.; Ge, Y. Comprehensive characterization of AMP-activated protein kinase catalytic domain by top-down mass spectrometry. J. Am. Soc. Mass Spectrom. 2016, 27(2): 220-232 Article

  55. 2015

  56. Gregorich Z. R.; Peng, Y.; Wolff, J. J.; Guo, W.; Guner, H.; Doop, J.; Hacker, T. A.; Ge, Y. Comprehensive assessment of regional and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. J. Mol. Cell. Cardiol. 2015, 87, 103-112. Article
  57. Chen, Y.-C.; Ayaz-Guner, S.; Peng, Y.; Lane, M. L.; Locher, M.; Larsson, L.; Kohmoto, T.; Moss, R. L.; Ge, Y. A top-down LC/MS+ method for assessing actin isoforms as a potential cardiac disease marker. Anal Chem. 2015, 87(16): 8399-406. Article

  58. Chang, Y. H.; Ye, L.; Cai, W.; Lee, Y.; Guner, H.; Lee, Y.; Kamp, T. J.; Zhang, J.; Ge, Y. Quantitative Proteomics Reveals Differential Regulation of Protein Expression in Recipient Myocardium after Trilineage Cardiovascular Cell Transplantation. Proteomics. 2015, 15, 2560-2567 DOI: 10.1002/pmic.201500131. Article

  59. Valeja, S. G.; Xiu, L.; Gregorich, Z. R.; Guner, H.; Jin, S.; Ge, Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem. 2015, 87(10), 5363-71. Article

  60. Hwang, L.; Ayaz-Guner, S.; Cai, W.; Gregorich Z. R.; Jin, S.; Ge, Y. Specific enrichment of phosphoproteins using functionalized multivalent nanoparticles. J. Am. Chem. Soc., 2015, 87, 5363-5371. Article

  61. Chang, Y.; Gregorich Z. R.; Chen, A. J.; Hwang L.; Guner, H.; Yu, D.; Zhang, J.; Ge, Y. New mass spectrometry-compatible degradable surfactant for tissue proteomics. J. Proteome Res., 2015, 14, 1587-1599. Article

  62. Chen, Y.; Sumandea, M. P.; Larsson, L.; Moss, R. L.; Ge, Y. Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. J. Muscle Res. Cell Motil., 2015, 36, 168-181. Article
  63. 2014

  64. Ye, L.; Chang, Y. H.; Xiong Q.; Zhang P.; Somasundaram, P.; Lepley M.; Swingen C.; Su, L.; Wendel, J. S.; Guo, J.; Jang, A.; Rosenbush, D.; Zhang, L.; Greder, L.; Dutton, J. R.; Zhang, J.; Kamp, T. J.; Kaufman, D.S.; Ge, Y.; Zhang, J. Cardiac repair in a porcine model of acute myocardial infarction with human induced pluripotent stem cell-derived cardiovascular cells. Cell Stem Cell, 2014, 15, 750-761. Article

  65. Peng, Y.; Gregorich Z. R.; Valeja, S. G.; Zhang, H.; Cai, W.; Chen, Y.; Guner, H.; Chen, A. J.; Schwahn, D. J.; Hacker, T. A.; Liu, X.; Ge, Y. Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction. Mol. Cell. Proteomics, 2014, 13, 2752-2764. Article

  66. Ge, Y.; Van Eyk, J. Cardiovascular disease: the leap towards translational and clinical proteomics. Proteomics Clin. Appl., 2014, 8, 473-475. Article
  67. Xiu, L.; Valeja, S. G.; Alpert, A. J.; Jin, S.; Ge, Y. Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics. Anal. Chem. 2014, 86, 7899-7906. Article

  68. Valkevich, E. M.; Sanchez, N.; Ge, Y.; Strieter, E. R. Middle-down mass spectrometry enables characterization of branched ubiquitin chains. Biochemistry, 2014, 53, 4979−4989. Article

  69. Peng, Y.; Ayaz-Guner, S.; Yu, D.; Ge, Y. Top-down mass spectrometry of cardiac myofilament proteins in health and disease, Proteomics Clin. Appl. 2014, 8, 554–568. Article
  70. Gregorich Z. R.; Ge, Y. Top-down proteomics in health and disease: challenges and opportunities, Proteomics, 2014, 14, 1195-1210. *This is an invited article for a special issue on “Top-down proteomics”. Article
  71. Gregorich Z. R.; Chang, Y.-W.; Ge, Y. Proteomics in heart failure: top-down or bottom-up? Pflugers Arch. Eur. J. Physiol. 2014, 466, 1199-1209. *This is an invited review for a special issue on “Heart Failure”. Article
  72. Witayavanitkul, N.; Sarkey, J.; Mou, Y. A.; Kuster, D.W.D.; Khairallah, R. J.; Govindan, S.; Chen, X.; Ge, Y.; Rajan, S.; Wieczorek, D. F.; Irving, T.; de Tombe, P. P.; Sadayappan, S. Myocardial infarction-induced N-terminal fragment of cMyBP-C impairs myofilament function in human left ventricular myofibrils, J. Biol. Chem. 2014, 289, 8818-8827 Article
  73. Chen, S.; Zhu, P.; Guo, H.; Wang, Y.; Ma, Y.; Wang, J.; Gao, J.; Chen, J.; Ge, Y.; Zhuang, J.; Li, J. Alpha-1 catalytic subunit of AMPK modulates contractile function of cardiomyocytes through phosphorylation of troponin I, Life Sci., 2014, 98, 75-82. Article
  74. Guner, H.; Close, P.L.; Cai, W.; Zhang, H.; Peng, Y.; Chen, Y.; Gregorich, Z. R. Ge, Y. MASH Suite: A user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization, J. Am. Soc. Mass Spectrom. 2014, 25, 464-470. Article

  75. 2013

  76. Zhao, D. S.; Gregorich Z. R.; Ge, Y. High throughput screening of disulfide-containing proteins in a complex mixture, Proteomics, 2013, 13, 3256-3260. Article
  77. Peng, Y.; Yu, D.; Gregorich Z., Chen, X.; Beyer, A. M.; Gutterman, D. D.; Ge, Y. In-depth proteomic analysis of human tropomyosin by top-down mass spectrometry, J. Muscle Res. Cell Motil. 2013, 34, 199-210. *This is an invited article for a special edition on “Tropomyosin: form and function”. Article
  78. Miao, J.; Lawrence, M.; Jeffers, V.; Zhao, F.; Parker, D.; Ge, Y.; Sullivan, W. J.; Cui, L. Extensive lysine acetylation occurs in evolutionarily conserved metabolic pathways and parasite-specific functions during Plasmodium falciparum intraerythrocytic development, Mol. Microbiol. 2013, 89, 660-675. Article
  79. Chen, X.; Ge, Y. Ultra-high pressure fast size exclusion chromatography for top-down proteomics, Proteomics, 2013, 13, 2563-2566. Article
  80. Smith LM, Kelleher NL; Consortium for Top Down Proteomics (Linial M, Goodlett D, Langridge-Smith P, Goo YA, Safford G, Bonilla L, Kruppa G, Zubarev R, Rontree J, Chamot-Rooke J, Garavelli J, Heck A, Loo J, Penque D, Hornshaw M, Hendrickson C, Pasa-Tolic L, Borchers C, Chan D, Young N, Agar J, Masselon C, Gross M, McLafferty F, Tsybin Y, Ge Y, Sanders I, Langridge J, Whitelegge J, Marshall A.), Proteoform: a single term describing protein complexity. Nat Methods. 2013, 10, 186-187. Article
  81. Guy, M. J.; Chen, Y.; Clinton, L.; Zhang, H.; Zhang, J.; Dong, X.; Xu, Q.; Ayaz-Guner, S.; Ge, Y. The impact of antibody selection on the detection of cardiac troponin I, Clin. Chim. Acta. 2013, 420, 82-88. *This is an invited article for a special issue on “Mass Spectrometry for Clinical Diagnosis”. Article
  82. Peng, Y.; Chen, X.; Zhang, H.; Xu, Q.; Hacker, T. A.; Ge, Y. Top-down targeted proteomics for deep sequencing of tropomyosin isoforms, J. Proteome Res. 2013, 12, 187-198. Article
  83. 2012

  84. Trang, V. H.; Valkevich, E. M.; Minami, S.; Chen, Y.; Ge, Y.; Strieter, E. R. Nonenzymatic polymerization of ubiquitin: single-step synthesis and isolation of discrete ubiquitin oligomers, Angew. Chem. Int. Ed. 2012, 124, 13262-13265. Article
  85. Yang, C.; Park, A. C.; Davis, N. A,; Russell, J. D.; Kim, B.; Brand, D. D.; Lawrence, M. J.; Ge, Y.; Coon, J. J.; Greenspan, D. S.; Comprehensive mass spectrometric mapping of the hydroxylated amino acid residues of the a1(V) collagen chain, J. Biol. Chem. 2012, 287, 40598-40610 Article
  86. Jia, C.; Hui, L.; Cao, W.; Lietz, C. B.; Jiang, X.; Chen, R.; Catherman, A. D.; Thomas, P. M.; Ge, Y.; Kelleher, N. L.; Li.; L. High-definition de novo sequencing of crustacean hyperglycemic hormone (CHH)-family neuropeptides, Mol. Cell Proteomics, 2012, 11, 1951-64. Article
  87.  Ge, Y.; Moss, R. L. Nitroxyl, redox switches, cardiac myofilaments, and heart failure: A prequel to novel therapeutics? Circ. Res. 2012, 111, 954-956. Article
  88. 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. Article
  89.  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., 2012, 110, 1192-1201.
  90. 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.
  91. 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.
  92.  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.
  93.  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.
  94. 2011

  95. 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”.
  96. 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.
  97. Zhang, J.; Zhang, H.; 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.
  98. Sancho Solis, R.; 41. Guy, M. J.; Chen, Y.; Clinton, L.; Zhang, H.; Zhang, J.; Dong, X.; Xu, Q.; Ayaz-Guner, S.; Ge, Y. The impact of antibody selection on the detection of cardiac troponin I, Clin. Chim. Acta. Accepted. *This is an invited article.
  99. 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.
  100. 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.
  101. 2010

  102. 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.
  103. 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. * This is an invited article featured on the cover of the journal.
  104. 2009

  105. 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.
  106. 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. *This article is a PNAS Direct Submission (Track II).
  107. 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.
  108. 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.
  109. 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.
  110. 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.
  111. 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.
  112. 2008

  113. 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.
  114. 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.

Prior to UW-Madison:

2001-2005
  1. 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.
  2. 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 b-keto sulfones: selective inhibitors of 11b–hydroxyster oid dehydrogenase type I, Bioorg. Med. Chem. Lett. 2005, 15, 2865-2869.
  3. Ge, Y.; Lawhorn, B. G.; ElNaggar, M.; Sze, S. K.; Begley, T. P.; McLafferty, F. W. Detection of four oxidation sites in viral prolyl-4-hydroxylase by top-down mass spectrometry, Protein Sci. 2003, 12, 2320-2326.
  4. 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.
  5. Sze, S. K.; Ge, Y.; Oh, H.; McLafferty, F. W. Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry Anal. Chem. 2003, 75, 1599-1603.
  6. 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.
  7. 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.
  8. 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
  9. Xi, J.; Ge, Y.; Kinsland, C. L.; McLafferty, F. W.; Begley, T. P. Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: identification of an 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.
  10. 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.
  11. 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.
  12. McLafferty, F. W.; Horn, D. M.; Breuker, K.; Ge, Y.; Cerda, B., A. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance, J. Am. Soc. Mass Spectrom. 2001, 12, 245-249.
  13. Strauss, E.; Kinsland, C.; Ge, Y.; McLafferty, F. W.; Begley, T. P. Phosphopantothenoylcysteine synthetase from Escherichia coli: Identification and characterization of the last unidentified coenzyme A biosynthetic enzyme in bacteria. J. Biol. Chem. 2001, 276, 13513-13516.
  14. 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.