Publications and Presentations by Human Proteomics Program (HPP) Staff and Users with the Data Acquired at HPP Mass Spectrometry Facility



  1. 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.

  2. 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.

  3. Friend, K., Campbell, Z.T., Cooke, A., Kroll-Conner, P., Wickens, M.P. and J. Kimble (2012) A conserved PUF/Ago/eEF1A complex attenuates translation elongation. Nature Structural and Molecular Biology 19(2), 176-183.

  4. 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.

  5. 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.

  6. 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.

  7. Ge, Y.; Moss, R. L. Nitroxyl, redox switches, cardiac myofilaments, and heart failure: A prequel to novel therapeutics? Circ. Res. 2012, 111, 954-956.

  8. 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.

  9. 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 α1(V) collagen chain, J. Biol. Chem. 2012, Epub ahead of print.

  10. 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, Epub ahead of print.

  11. 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.


  1. Hoffmann, B.R.; Annis, D.S.; Mosher, D.F.  Reactivity of the N-terminal Region of Fibronectin Protein to Transglutaminase 2 and Factor XIIIA, J. Biol. Chem. 2011, 286, 32220-30.

  2. Wei, X.; Herbst, A.; Ma, D.; Aiken, J.; Li, L. A quantitative proteomic approach to prion disease biomarker research: delving into the glycoproteome. J. Proteome Res., 2011, 10, 2687-2702.

  3. 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.

  4. 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.

  5. 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.

  6. 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.  

  7. 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.

  8. 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”.


  1. 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.

  2. Wei, X.; Dulberger, C.; Li, L. Characterization of murine brain membrane glycoproteins by detergent assisted lectin affinity chromatography (DALAC). Anal. Chem., 82, 6329-6333.

  3. 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.

  4. Xu, J.;  Maurer, L.M.; Hoffmann, B.R.; Annis, D.S.; Mosher, D.F.  IsoDGR sequence do not mediate binding of fibronectin N-terminal modules to adherent fibronectin-null fibroblasts,  J. Biol. Chem. 2010, 19, 285, 8563-8571.


  1. 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.

  2. Wei, X.; Herbst, A.; Schmidt, J.; Aiken, J.; Li, L. Facilitating discovery of prion disease biomarkers by quantitative glycoproteomics. LCGC [Invited technical article, February 2009 issue]
  3. 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.

  4. 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, 22, 479-488.

  5. 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.

  6. 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.

  7. 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.

  8. 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, 2009, 29, 2161-2168.

  9. Dowell, J.A., Johnson, J.A., Li, L. Identification of astrocyte secreted proteins with a combination of shotgun proteomics and bioinformatics. J. Proteome Res., 2009, 8, 4135-4143.


  1. 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.
  2. Berndsen, C.E.;  Tsubota, T.; Lindner, S.E.; Lee, S.; Holton, J.M.; Kaufman, P.D.; Keck, J.L.; Denu, J.M. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nat. Struct. Mol. Biol. 2008, 15, 948-956.

  3. Lee, S.; Tong, L.; Denu, J.M.  Quantification of endogenous sirtuin metabolite O-Acetyl-ADP-Ribose (OAADPR). Anal. Biochem. 2008, 383, 174-179.
  4. 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.