Publications

Crowe SO, Rana A, Deol KK, Ge Y, Strieter ER. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in CellulO. Analytical Chemistry. 2017;89:4428-4434.
Jin YT, Wei LM, Cai WX, Lin ZQ, Wu ZJ, Peng Y, et al.. Complete Characterization of Cardiac Myosin Heavy Chain (223 kDa) Enabled by Size-Exclusion Chromatography and Middle-Down Mass Spectrometry. Analytical Chemistry. 2017;89:4922-4930.
Cai WX, Tucholski T, Chen BF, Alpert AJ, McIlwain S, Kohmoto T, et al.. Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Analytical Chemistry. 2017;89:5467-5475.
Yang LB, Gregorich ZR, Cai WX, Zhang P, Young B, Gu YW, et al.. Quantitative Proteomics and Immunohistochemistry Reveal Insights into Cellular and Molecular Processes in the Infarct Border Zone One Month after Myocardial Infarction. Journal of Proteome Research. 2017;16:2101-2112.
Chen BF, Hwang L, Ochowicz W, Lin ZQ, Guardado-Alvarez TM, Cai WX, et al.. Coupling functionalized cobalt ferrite nanoparticle enrichment with online LC/MS/MS for top-down phosphoproteomics. Chemical Science. 2017;8:4306-4311.
Gregorich ZR, Cai WX, Lin ZQ, Chen AJ, Peng Y, Kohmoto T, et al.. Distinct sequences and post-translational modifications in cardiac atrial and ventricular myosin light chains revealed by top-down mass spectrometry. Journal of Molecular and Cellular Cardiology. 2017;107:13-21.
Chen BF, Guo X, Tucholski T, Lin ZQ, McIlwain S, Ge Y. The Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective. Journal of the American Society for Mass Spectrometry. 2017;28:1805-1814.
Rana A, Ge Y, Strieter ER. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry (UbiChEM-MS) Reveals Cell-Cycle Dependent Formation of Lys11/Lys48 Branched Ubiquitin Chains. Journal of Proteome Research. 2017;16:3363-3369.
Yu DY, Peng Y, Ayaz-Guner S, Gregorich ZR, Ge Y. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry. Journal of the American Society for Mass Spectrometry. 2016;27:220-232.
Jin YT, Peng Y, Lin ZQ, Chen YC, Wei LM, Hacker TA, et al.. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. Journal of Muscle Research and Cell Motility. 2016;37:41-52.
Hwang L, Guardado-Alvarez TM, Ayaz-Gunner S, Ge Y, Jin S. A Family of Photolabile Nitroveratryl-Based Surfactants That Self-Assemble into Photodegradable Supramolecular Structures. Langmuir. 2016;32:3963-3969.
Gregorich ZR, Peng Y, Cai WX, Jin YT, Wei LM, Chen AJ, et al.. Top-Down Targeted Proteomics Reveals Decrease in Myosin Regulatory Light-Chain Phosphorylation That Contributes to Sarcopenic Muscle Dysfunction. Journal of Proteome Research. 2016;15:2706-2716.
Crowe SO, Pham GH, Ziegler JC, Deol KK, Guenette RG, Ge Y, et al.. Subunit-Specific Labeling of Ubiquitin Chains by Using Sortase: Insights into the Selectivity of Deubiquitinases. Chembiochem. 2016;17:1525-1531.
Gregorich ZR, Peng Y, Lane NM, Wolff JJ, Wang SJ, Guo W, et al.. Comprehensive assessment of chamber-specific and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. Journal of Molecular and Cellular Cardiology. 2015;87:102-112.
Hwang L, Ayaz-Guner S, Gregorich ZR, Cai WX, Valeja SG, Jin S, et al.. Specific Enrichment of Phosphoproteins Using Functionalized Multivalent Nanoparticles. Journal of the American Chemical Society. 2015;137:2432-2435.
Chang YH, Gregorich ZR, Chen AJ, Hwang LY, Guner H, Yu DY, et al.. New Mass-Spectrometry-Compatible Degradable Surfactant for Tissue Proteomics. Journal of Proteome Research. 2015;14:1587-1599.
Chen YC, Sumandea MP, Larsson L, Moss RL, Ge Y. Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. Journal of Muscle Research and Cell Motility. 2015;36:169-181.
Valeja SG, Xiu LC, Gregorich ZR, 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. Analytical Chemistry. 2015;87:5363-5371.
Chang YH, Ye L, Cai WX, Lee Y, Guner H, Lee Y, et al.. Quantitative proteomics reveals differential regulation of protein expression in recipient myocardium after trilineage cardiovascular cell transplantation. Proteomics. 2015;15:2560-2567.
Chen YC, Ayaz-Guner S, Peng Y, Lane NM, Locher MR, Kohmoto T, et al.. Effective Top-Down LC/MS plus Method for Assessing Actin Isoforms as a Potential Cardiac Disease Marker. Analytical Chemistry. 2015;87:8399-8406.
Valkevich EM, Sanchez NA, Ge Y, Strieter ER. Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains. Biochemistry. 2014;53:4979-4989.
Peng Y, Ayaz-Guner S, Yu DY, Ge Y. Top-down mass spectrometry of cardiac myofilament proteins in health and disease. Proteomics Clinical Applications. 2014;8:554-568.
Xiu LC, Valeja SG, Alpert AJ, Jin S, Ge Y. Effective Protein Separation by Coupling Hydrophobic Interaction and Reverse Phase Chromatography for Top-down Proteomics. Analytical Chemistry. 2014;86:7899-7906.
Witayavanitkul N, Mou YAit, Kuster DWD, Khairallah RJ, Sarkey J, Govindan S, et al.. Myocardial Infarction-induced N-terminal Fragment of Cardiac Myosin-binding Protein C ( cMyBP-C) Impairs Myofilament Function in Human Myocardium. Journal of Biological Chemistry. 2014;289:8818-8827.
Peng Y, Gregorich ZR, Valeja SG, Zhang H, Cai WX, Chen YC, et al.. Top-down Proteomics Reveals Concerted Reductions in Myofilament and Z-disc Protein Phosphorylation after Acute Myocardial Infarction. Molecular & Cellular Proteomics. 2014;13:2752-2764.
Ye L, Chang YH, Xiong Q, Zhang PY, Zhang LY, Somasundaram P, et al.. 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.
Guner H, Close PL, Cai WX, Zhang H, Peng Y, Gregorich ZR, et al.. MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization. Journal of the American Society for Mass Spectrometry. 2014;25:464-470.
Gregorich ZR, Ge Y. Top-down proteomics in health and disease: Challenges and opportunities. Proteomics. 2014;14:1195-1210.
Gregorich ZR, Chang YH, Ge Y. Proteomics in heart failure: top-down or bottom-up?. Pflugers Arch. Eur. J. Physiol. 2014;466:1199-1209.
Chen S, Zhu P, Guo H-M, Solis RSancho, Wang Y, Ma Y, et al.. Alpha1 catalytic subunit of AMPK modulates contractile function of cardiomyocytes through phosphorylation of troponin I. Life Sciences. 2014;98:75-82.
Zhao DS, Gregorich ZR, Ge Y. High throughput screening of disulfide-containing proteins in a complex mixture. Proteomics. 2013;13:3256-3260.
Peng Y, Yu DY, Gregorich Z, Chen X, Beyer AM, Gutterman DD, et al.. In-depth proteomic analysis of human tropomyosin by top-down mass spectrometry. Journal of Muscle Research and Cell Motility. 2013;34:199-210.
Peng Y, Chen X, Zhang H, Xu QG, Hacker TA, Ge Y. Top-down Targeted Proteomics for Deep Sequencing of Tropomyosin Isoforms. Journal of Proteome Research. 2013;12:204-215.
Miao J, Lawrence M, Jeffers V, Zhao F, Parker D, Ge Y, et al.. Extensive lysine acetylation occurs in evolutionarily conserved metabolic pathways and parasite-specific functions during Plasmodium falciparum intraerythrocytic development. Molecular Microbiology. 2013;89:660-675.
Guy MJ, Chen Y-C, Clinton L, Zhang H, Zhang J, Dong X, et al.. The impact of antibody selection on the detection of cardiac troponin I. Clinica Chimica Acta. 2013;420:82-88.
Chen X, Ge Y. Ultrahigh pressure fast size exclusion chromatography for top-down proteomics. Proteomics. 2013;13:2563-2566.
Wang YC, Pinto JR, Solis RS, Dweck D, Liang JS, Diaz-Perez Z, et al.. Generation and Functional Characterization of Knock-in Mice Harboring the Cardiac Troponin I-R21C Mutation Associated with Hypertrophic Cardiomyopathy. Journal of Biological Chemistry. 2012;287:2156-2167.
Valkevich EM, Guenette RG, Sanchez NA, Chen YC, Ge Y, Strieter ER. Forging Isopeptide Bonds Using Thiol-Ene Chemistry: Site-Specific Coupling of Ubiquitin Molecules for Studying the Activity of Isopeptidases. Journal of the American Chemical Society. 2012;134:6916-6919.
Peng Y, Chen X, Sato T, Rankin SA, Tsuji RF, Ge Y. Purification and High-Resolution Top-Down Mass Spectrometric Characterization of Human Salivary alpha-Amylase. Analytical Chemistry. 2012;84:3339-3346.
Oliveira SM, Zhang YH, Solis RS, Isackson H, Bellahcene M, Yavari A, et al.. AMP-Activated Protein Kinase Phosphorylates Cardiac Troponin I and Alters Contractility of Murine Ventricular Myocytes. Circulation Research. 2012;110:1192-1201.
Jia CX, Hui LM, Cao WF, Lietz CB, Jiang XY, Chen RB, et al.. High-definition De Novo Sequencing of Crustacean Hyperglycemic Hormone (CHH)-family Neuropeptides. Molecular & Cellular Proteomics. 2012;11:1951-1964.
Du JH, Teng RJ, Lawrence M, Guan TJ, Xu H, Ge Y, et al.. The Protein Partners of GTP Cyclohydrolase I in Rat Organs. Plos One. 2012;7.
Dong XT, Sumandea CA, Chen YC, Garcia-Cazarin ML, Zhang J, Balke CW, et al.. Augmented Phosphorylation of Cardiac Troponin I in Hypertensive Heart Failure. Journal of Biological Chemistry. 2012;287:848-857.
Yang C, Park AC, Davis NA, Russell JD, Kim B, Brand DD, et al.. Comprehensive Mass Spectrometric Mapping of the Hydroxylated Amino Acid residues of the α1(V) Collagen Chain. Journal of Biological Chemistry. 2012;287:40598-40610.
Trang VH, Valkevich EM, Minami S, Chen Y-C, Ge Y, Strieter ER. Nonenzymatic Polymerization of Ubiquitin: Single-Step Synthesis and Isolation of Discrete Ubiquitin Oligomers. Angewandte Chemie-International Edition. 2012;51:13085-13088.
Ge Y, Moss RL. Nitroxyl, Redox Switches, Cardiac Myofilaments, and Heart Failure: A Prequel to Novel Therapeutics?. Circulation Research. 2012;111:954-956.
Zhang J, Zhang H, Ayaz-Guner S, Chen YC, Dong XT, Xu QG, et al.. Phosphorylation, but Not Alternative Splicing or Proteolytic Degradation, Is Conserved in Human and Mouse Cardiac Troponin T. Biochemistry. 2011;50:6081-6092.
Zhang J, Guy MJ, Norman HS, Chen YC, Xu QG, Dong XT, et al.. Top-Down Quantitative Proteomics Identified Phosphorylation of Cardiac Troponin I as a Candidate Biomarker for Chronic Heart Failure. Journal of Proteome Research. 2011;10:4054-4065.
Zhang H, Ge Y. Comprehensive Analysis of Protein Modifications by Top-Down Mass Spectrometry. Circulation-Cardiovascular Genetics. 2011;4:711-+.
Xu FM, Xu QG, Dong XT, Guy M, Guner H, Hacker TA, et al.. Top-down high-resolution electron capture dissociation mass spectrometry for comprehensive characterization of post-translational modifications in Rhesus monkey cardiac troponin I. International Journal of Mass Spectrometry. 2011;305:95-102.
Solis RS, Ge Y, Walker JW. A preferred AMPK phosphorylation site adjacent to the inhibitory loop of cardiac and skeletal troponin I. Protein Science. 2011;20:894-907.
Kuhn P, Chumanov R, Wang YD, Ge Y, Burgess RR, Xu W. Automethylation of CARM1 allows coupling of transcription and mRNA splicing. Nucleic Acids Research. 2011;39:2717-2726.
Zhang JA, Dong XT, Hacker TA, Ge Y. Deciphering Modifications in Swine Cardiac Troponin I by Top-Down High-Resolution Tandem Mass Spectrometry. Journal of the American Society for Mass Spectrometry. 2010;21:940-948.
Nelson CA, Szczech JR, Dooley CJ, Xu QG, Lawrence MJ, Zhu HY, et al.. Effective Enrichment and Mass Spectrometry Analysis of Phosphopeptides Using Mesoporous Metal Oxide Nanomaterials. Analytical Chemistry. 2010;82:7193-7201.
Nelson CA, Szczech JR, Xu QG, Lawrence MJ, Jin S, Ge Y. Mesoporous zirconium oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics. Chemical Communications. 2009;:6607-6609.
Ma MM, Chen RB, Ge Y, He H, Marshall AG, Li LJ. Combining Bottom-Up and Top-Down Mass Spectrometric Strategies for De Novo Sequencing of the Crustacean Hyperglycemic Hormone from Cancer borealis. Analytical Chemistry. 2009;81:240-247.
Liu L, Hou J, Du JL, Chumanov RS, Xu QG, Ge Y, et al.. Differential modification of Cys10 alters transthyretin's effect on beta-amyloid aggregation and toxicity. Protein Engineering Design & Selection. 2009;22:479-488.
Kuhn P, Xu QG, Cline E, Zhang D, Ge Y, Xu W. Delineating Anopheles gambiae coactivator associated arginine methyltransferase 1 automethylation using top-down high resolution tandem mass spectrometry. Protein Science. 2009;18:1272-1280.
Ge Y, Rybakova IN, Xu QG, Moss RL. Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state. Proceedings of the National Academy of Sciences of the United States of America. 2009;106:12658-12663.
Du JH, Wei N, Xu H, Ge Y, Vasquez-Vivar J, Guan TJ, et al.. Identification and Functional Characterization of Phosphorylation Sites on GTP Cyclohydrolase I. Arteriosclerosis Thrombosis and Vascular Biology. 2009;29:2161-U385.
Ayaz-Guner S, Zhang J, Li L, Walker JW, 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.
Zabrouskov V, Ge Y, Schwartz J, Walker JW. Unraveling Molecular Complexity of Phosphorylated Human Cardiac Troponin I by Top Down Electron Capture Dissociation/Electron Transfer Dissociation Mass Spectrometry. Molecular & Cellular Proteomics. 2008;7:1838-1849.
Solis RS, Ge Y, Walker JW. Single amino acid sequence polymorphisms in rat cardiac troponin revealed by top-down tandem mass spectrometry. Journal of Muscle Research and Cell Motility. 2008;29:203-212.
Colabroy KL, Zhai HL, Li TF, Ge Y, Zhang Y, Liu AM, et al.. The mechanism of inactivation of 3-hydroxyanthranilate-3,4-dioxygenase by 4-chloro-3-hydroxyanthranilate. Biochemistry. 2005;44:7623-7631.
Xiang J, Ipek M, Suri V, Massefski W, Pan N, Ge Y, et al.. Synthesis and biological evaluation of sulfonamidooxazoles and beta-keto sulfones: selective inhibitors of 11 beta-hydroxysteroid dehydrogenase type I. Bioorganic & Medicinal Chemistry Letters. 2005;15:2865-2869.
Sze SK, Ge Y, Oh HB, McLafferty FW. Plasma electron capture characterization of large dissociation for the proteins by top down mass spectrometry. Analytical Chemistry. 2003;75:1599-1603.
Ge Y, Lawhorn BG, ElNaggar M, Sze SK, Begley TP, McLafferty FW. Detection of four oxidation sites in viral prolyl-4-hydroxylase by top-down mass spectrometry. Protein Science. 2003;12:2320-2326.
Ge Y, ElNaggar M, Sze SK, Bin Oh H, Begley TP, McLafferty FW, et al.. Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry. Journal of the American Society for Mass Spectrometry. 2003;14:253-261.
Sze SK, Ge Y, Oh H, McLafferty FW. Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proceedings of the National Academy of Sciences of the United States of America. 2002;99:1774-1779.
Oh H, Breuker K, Sze SK, Ge Y, Carpenter BK, McLafferty FW. Secondary and tertiary structures of gaseous protein ions characterized by electron capture dissociation mass spectrometry and photofragment spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 2002;99:15863-15868.
Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, et al.. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. Journal of the American Chemical Society. 2002;124:672-678.
Xi J, Ge Y, Kinsland C, McLafferty FW, Begley TP. 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. Proceedings of the National Academy of Sciences of the United States of America. 2001;98:8513-8518.
Strauss E, Kinsland C, Ge Y, McLafferty FW, Begley TP. Phosphopantothenoylcysteine synthetase from Escherichia coli - Identification and characterization of the last unidentified coenzyme A biosynthetic enzyme in bacteria. Journal of Biological Chemistry. 2001;276:13513-13516.
McLafferty FW, Horn DM, Breuker K, Ge Y, Lewis MA, Cerda B, et al.. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. Journal of the American Society for Mass Spectrometry. 2001;12:245-249.
Ge Y, Horn DM, McLafferty FW. Blackbody infrared radiative dissociation of larger (42 kDa) multiply charged proteins. International Journal of Mass Spectrometry. 2001;210:203-214.
Fred WM, David MH, Ge Y, Cerda B, Fridriksson E, Breuker K. New frontiers in molecular mass spectrometry. Adv. Mass Spectrom. 2001;15:167-173.
Horn DM, Ge Y, McLafferty FW. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Analytical Chemistry. 2000;72:4778-4784.