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

HPP users are kindly requested to acknowledge the HPP in all publications made possible, in whole or in part, by the facilities. Our suggested acknowledgement statement template is: "The authors would like to acknowledge the UW-Madison Human Proteomics Program Mass Spectrometry Facility (initially funded by the Wisconsin partnership funds) for support in obtaining mass spectrometry data and NIH S10OD018475 for the acquisition of ultra-high resolution mass spectrometer for biomedical research."

Publications:

2016

  1. 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., Epub ahead of Print. DOI: 10.1021/acs.jproteome.6b00244.

  2. 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., Epub ahead of print.

  3. Cai, W.; Tucholski, T. M.; Ge, Y. Top-down proteomics for comprehensive analysis of isoforms and post-translational modifications and its application to heart diseases. Expert Rev. Proteomics., Accepted.

  4. 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.

  5. 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.

  6. 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. /li>
  7. 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.

  8. 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

2015

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

2014

  1. 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.

  2. 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.

  3. Ge, Y.; Van Eyk, J. Cardiovascular disease: the leap towards translational and clinical proteomics. Proteomics Clin. Appl., 2014, 8, 473-475.

  4. 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.

  5. 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.

  6. 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.

  7. Gregorich Z. R.; Ge, Y. Top-down proteomics in health and disease: challenges and opportunities, Proteomics, 2014, 14, 1195-1210.

  8. 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.

  9. 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

  10. Chen, S.; Zhu, P.; Guo, H.; Wang, Y.; Ma, Y.; Wang, J.; Gao, J.; Chen, J.; Ge, Y.; Zhuang, J.; Li, J. a-1 catalytic subunit of AMPK modulates contractile function of cardiomyocytes through phosphorylation of troponin I, Life Sci., 2014, 98, 75-82.

  11. 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.

2013

  1. Zhao, D. S.; Gregorich Z. R.; Ge, Y. High throughput screening of disulfide-containing proteins in a complex mixture, Proteomics, 2013, 13, 3256-3260.

  2. 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.

  3. 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.

  4. Chen, X.; Ge, Y. Ultra-high pressure fast size exclusion chromatography for top-down proteomics, Proteomics, 2013, 13, 2563-2566.

  5. 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.

  6. 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.

  7. 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.

2012

  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.

2011

  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”.

2010

  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.

2009

  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.

2008

  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.