Top-down Proteomics: Technology Advancements and Applications to Heart Diseases
Open accessAbstract
INTRODUCTION: Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood. AREAS COVERED: Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.
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Mutations and differential expression of protein isoforms drive molecular mechanisms underlying disease phenotypes.
“Moreover, mutations and differential expression of protein isoforms have been shown to drive molecular mechanisms underlying disease phenotypes, necessitating their in-depth characterization [5,7].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [7]
MS-based proteomics has become a staple in biomedical research for discovering novel biomarkers and elucidating disease mechanisms.
“MS-based proteomics has become a staple in biomedical research for the discovery of novel biomarkers and elucidation of disease mechanisms [140].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [140]
Top-down mass spectrometry analyzes intact proteins and is the most powerful approach for comprehensive proteoform characterization, including post-translational modifications and sequence variants.
“In contrast, top-down mass spectrometry (MS)-based proteomics analyzes intact proteins and is the most powerful method to comprehensively characterize proteoforms deciphering the PTMs together with sequence variations1–3.”
From A photocleavable surfactant for top-down proteomics (2019) · cites this paper as [3]
Top-down proteomics allows direct analysis of intact proteins without digestion, providing a bird's-eye view of existing proteoforms.
“top-down proteomics allows for direct analysis of intact proteins without digestion, thus providing a “bird’s-eye” view of existing proteoforms (9, 12, 21, 23, 28, 29).”
From Distinct hypertrophic cardiomyopathy genotypes result in convergent sarcomeric proteoform profiles revealed by top-down proteomics (2020) · cites this paper as [9]
Proteoforms of interest can be fragmented by tandem MS for sequence characterization and PTM localization.
“Subsequently, proteoforms of interest can be fragmented by tandem MS (MS/MS) for sequence characterization and PTM localization (9, 21, 23).”
From Distinct hypertrophic cardiomyopathy genotypes result in convergent sarcomeric proteoform profiles revealed by top-down proteomics (2020) · cites this paper as [9]
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Cites
Electrospray Ionization for Mass Spectrometry of Large Biomolecules
Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., & Whitehouse, C. M. (1989) · Science · doi:10.1126/science.2675315 · Cited by 7,634 · see citing works
Heart Disease and Stroke Statistics—2015 Update: A Report From the American Heart Association
Mozaffarian, D., Benjamin, E. J., Go, A. S., Arnett, D. K., Blaha, M. J., Cushman, M., de Ferranti, S., Després, J.-P., Fullerton, H. J., Howard, V. J., et al. (2015) · Circulation · doi:10.1161/cir.0000000000000152 · Cited by 5,797 · see citing works
Proteomics to study genes and genomes
Pandey, A., & Mann, M. (2000) · Nature · doi:10.1038/35015709 · Cited by 2,373 · see citing works
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., & Hunt, D. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402700101 · Cited by 2,370 · see citing works
Proteomic analysis of post-translational modifications
Mann, M., & Jensen, O. N. (2003) · Nature Biotechnology · doi:10.1038/nbt0303-255 · Cited by 2,136 · see citing works
Epidemiology and risk profile of heart failure
Bui, A. L., Horwich, T. B., & Fonarow, G. C. (2011) · Nature Reviews Cardiology · doi:10.1038/nrcardio.2010.165 · Cited by 2,077 · see citing works
Proteoform: a single term describing protein complexity
The Consortium for Top Down Proteomics, Smith, L. M., & Kelleher, N. L. (2013) · Nature Methods · doi:10.1038/nmeth.2369 · Cited by 1,528 · see citing works
Marty, M. T., Baldwin, A. J., Marklund, E. G., Hochberg, G. K. A., Benesch, J. L. P., & Robinson, C. V. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00140 · Cited by 1,000 · see citing works
Activation of Protein Kinase C Isoforms and Its Impact on Diabetic Complications
Geraldes, P., & King, G. L. (2010) · Circulation Research · doi:10.1161/circresaha.110.217117 · Cited by 993 · see citing works
Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis
Makarov, A. (2000) · Analytical Chemistry · doi:10.1021/ac991131p · Cited by 991 · see citing works
Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations
Zubarev, R. A., Horn, D. M., Fridriksson, E. K., Kelleher, N. L., Kruger, N. A., Lewis, M. A., Carpenter, B. K., & McLafferty, F. W. (2000) · Analytical Chemistry · doi:10.1021/ac990811p · Cited by 986 · see citing works
The Age of Crosstalk: Phosphorylation, Ubiquitination, and Beyond
Hunter, T. R. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.11.019 · Cited by 946 · see citing works
McMurray, J. J. V., & Pfeffer, M. A. (2005) · The Lancet · doi:10.1016/s0140-6736(05)66621-4 · Cited by 835 · see citing works
Mapping intact protein isoforms in discovery mode using top-down proteomics
Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E., Catherman, A. D., Durbin, K. R., Tipton, J. D., Vellaichamy, A., Kellie, J. F., Li, M., et al. (2011) · Nature · doi:10.1038/nature10575 · Cited by 665 · see citing works
Ion Formation in MALDI: The Cluster Ionization Mechanism
Karas, M., & Krüger, R. (2003) · Chemical Reviews · doi:10.1021/cr010376a · Cited by 648 · see citing works
Correlations between RNA and protein expression profiles in 23 human cell lines
Gry, M., Rimini, R., Strömberg, S., Asplund, A., Pontén, F., Uhlén, M., & Nilsson, P. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-365 · Cited by 520 · see citing works
Orbitrap mass spectrometry: Instrumentation, ion motion and applications
Perry, R. H., Cooks, R. G., & Noll, R. J. (2008) · Mass Spectrometry Reviews · doi:10.1002/mas.20186 · Cited by 515 · see citing works
Automated reduction and interpretation of
Horn, D. M., Zubarev, R. A., & McLafferty, F. W. (2000) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(99)00157-9 · Cited by 507 · see citing works
Decoding protein modifications using top-down mass spectrometry
Siuti, N., & Kelleher, N. L. (2007) · Nature Methods · doi:10.1038/nmeth1097 · Cited by 503 · see citing works
Senko, M. W., Beu, S. C., & McLaffertycor, F. W. (1995) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(95)00017-8 · Cited by 451 · see citing works
Precision proteomics: The case for high resolution and high mass accuracy
Mann, M., & Kelleher, N. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800788105 · Cited by 450 · see citing works
Mass Spectrometry: Bottom-Up or Top-Down?
Chait, B. T. (2006) · Science · doi:10.1126/science.1133987 · Cited by 442 · see citing works
Mass spectrometry of intact membrane protein complexes
Laganowsky, A., Reading, E., Hopper, J. T. S., & Robinson, C. V. (2013) · Nature Protocols · doi:10.1038/nprot.2013.024 · Cited by 409 · see citing works
Tackling heart failure in the twenty-first century
Mudd, J. O., & Kass, D. A. (2008) · Nature · doi:10.1038/nature06798 · Cited by 404 · see citing works
Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation
Shaw, J. B., Li, W., Holden, D. D., Zhang, Y., Griep-Raming, J., Fellers, R. T., Early, B. P., Thomas, P. M., Kelleher, N. L., & Brodbelt, J. S. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4029654 · Cited by 371 · see citing works
Karve, T. M., & Cheema, A. K. (2011) · Journal of Amino Acids · doi:10.4061/2011/207691 · Cited by 364 · see citing works
Ge, Y., Lawhorn, B. G., ElNaggar, M., Strauss, E., Park, J.-H., Begley, T. P., & McLafferty, F. W. (2002) · Journal of the American Chemical Society · doi:10.1021/ja011335z · Cited by 356 · see citing works
Self-citationExtending Top-Down Mass Spectrometry to Proteins with Masses Greater Than 200 Kilodaltons
Han, X., Jin, M., Breuker, K., & McLafferty, F. W. (2006) · Science · doi:10.1126/science.1128868 · Cited by 328 · see citing works
Cardiac Myosin Binding Protein C
Flashman, E., Redwood, C. S., Moolman‐Smook, J. C., & Watkins, H. C. (2004) · Circulation Research · doi:10.1161/01.res.0000127175.21818.c2 · Cited by 323 · see citing works
Zamdborg, L., LeDuc, R. D., Glowacz, K. J., Kim, Y.-B., Viswanathan, V., Spaulding, I. T., Early, B. P., Bluhm, E. J., Babai, S., & Kelleher, N. L. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm371 · Cited by 251 · see citing works
On the Scalability and Requirements of Whole Protein Mass Spectrometry
Compton, P. D., Zamdborg, L., Thomas, P. M., & Kelleher, N. L. (2011) · Analytical Chemistry · doi:10.1021/ac2010795 · Cited by 243 · see citing works
Pesavento, J. J., Mizzen, C. A., & Kelleher, N. L. (2006) · Analytical Chemistry · doi:10.1021/ac0600050 · Cited by 240 · see citing works
Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J. N., Anderson, G. A., & Smith, R. D. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-87 · Cited by 217 · see citing works
Top‐down proteomics in health and disease: Challenges and opportunities
Gregorich, Z. R., & Ge, Y. (2014) · PROTEOMICS · doi:10.1002/pmic.201300432 · Cited by 217 · see citing works
Self-citationTran, J. C., & Doucette, A. A. (2008) · Analytical Chemistry · doi:10.1021/ac702197w · Cited by 206 · see citing works
Mass Spectrometry of Protein Complexes: From Origins to Applications
Mehmood, S., Allison, T. M., & Robinson, C. V. (2015) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-040214-121732 · Cited by 200 · see citing works
Zhang, J., Guy, M. J., Norman, H. S., Chen, Y.-C., Xu, Q., Dong, X., Guner, H., Wang, S., Kohmoto, T., Young, K. H., et al. (2011) · Journal of Proteome Research · doi:10.1021/pr200258m · Cited by 194 · see citing works
Self-citationTop‐down MS, a powerful complement to the high capabilities of proteolysis proteomics
McLafferty, F. W., Breuker, K., Jin, M., Han, X., Infusini, G., Jiang, H., Kong, X., & Begley, T. P. (2007) · FEBS Journal · doi:10.1111/j.1742-4658.2007.06147.x · Cited by 187 · see citing works
Chamot-Rooke, J., Mikaty, G., Malosse, C., Soyer, M., Dumont, A., Gault, J., Imhaus, A.-F., Martin, P., Trellet, M., Clary, G., et al. (2011) · Science · doi:10.1126/science.1200729 · Cited by 180 · see citing works
Beck, S., Michalski, A., Raether, O., Lubeck, M., Kaspar, S., Goedecke, N., Baessmann, C., Hornburg, D., Meier, F., Paron, I., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.047407 · Cited by 173 · see citing works
Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins
Liu, X., Inbar, Y., Dorrestein, P. C., Wynne, C., Edwards, N., Souda, P., Whitelegge, J. P., Bafna, V., & Pevzner, P. A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002766 · Cited by 170 · see citing works
Catherman, A. D., Durbin, K. R., Ahlf, D. R., Early, B. P., Fellers, R. T., Tran, J. C., Thomas, P. M., & Kelleher, N. L. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.030114 · Cited by 157 · cited 1× · see citing works
“identified 1220 proteins, approximately 25% of which were membrane proteins, and over 5000 proteoforms from the H1299 human cell line [42], which represents the largest top-down proteomics analysis conducted to date.”
BackgroundAnsong, C., Wu, S., Meng, D., Liu, X., Brewer, H. M., Deatherage Kaiser, B. L., Nakayasu, E. S., Cort, J. R., Pevzner, P., Smith, R. D., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221210110 · Cited by 157 · see citing works
Detergent-free mass spectrometry of membrane protein complexes
Hopper, J. T. S., Yu, Y. T.-C., Li, D., Raymond, A., Bostock, M. J., Liko, I., Mikhailov, V. A., Laganowsky, A. D., Benesch, J. L. P., Caffrey, M., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2691 · Cited by 155 · see citing works
Ge, Y., Rybakova, I. N., Xu, Q., & Moss, R. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813369106 · Cited by 154 · see citing works
Self-citationProtein Identification Using Top-Down Spectra
Liu, X., Sirotkin, Y., Shen, Y., Anderson, G., Tsai, Y. S., Ting, Y. S., Goodlett, D. R., Smith, R. D., Bafna, V., & Pevzner, P. A. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.008524 · Cited by 153 · see citing works
Comprehensive Analysis of Protein Modifications by Top-Down Mass Spectrometry
Zhang, H., & Ge, Y. (2011) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.110.957829 · Cited by 148 · see citing works
Self-citationMASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics
Cai, W., Guner, H., Gregorich, Z. R., Chen, A. J., Ayaz-Guner, S., Peng, Y., Valeja, S. G., Liu, X., & Ge, Y. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o115.054387 · Cited by 132 · see citing works
Self-citationMultiplexed size separation of intact proteins in solution phase for mass spectrometry.
Tran, J. C., & Doucette, A. (2009) · Analytical Chemistry · doi:10.1021/ac900729r · Cited by 123 · see citing works
Unit resolution mass spectra of 112 kDa molecules with 3 Da accuracy
Kelleher, N. L., Senko, M. W., Siegel, M. M., & McLafferty, F. W. (1997) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(97)00060-3 · Cited by 122 · see citing works
Ion Parking during Ion/Ion Reactions in Electrodynamic Ion Traps
McLuckey, S. A., Reid, G. E., & Wells, J. M. (2001) · Analytical Chemistry · doi:10.1021/ac0109671 · Cited by 115 · see citing works
Sarcomeric protein isoform transitions in cardiac muscle: A journey to heart failure
Yin, Z., Ren, J. T., & Guo, W. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2014.11.003 · Cited by 115 · see citing works
Role of chromatographic techniques in proteomic analysis
Neverova, I., & Eyk, J. E. V. (2004) · Journal of Chromatography B · doi:10.1016/j.jchromb.2004.11.009 · Cited by 111 · see citing works
Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa
Durbin, K. R., Fornelli, L., Fellers, R. T., Doubleday, P. F., Narita, M., & Kelleher, N. L. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00997 · Cited by 111 · see citing works
Online Hydrophobic Interaction Chromatography–Mass Spectrometry for Top-Down Proteomics
Chen, B., Peng, Y., Valeja, S. G., Xiu, L., Alpert, A. J., & Ge, Y. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04285 · Cited by 110 · see citing works
Self-citationMass spectrometry-based proteomics for systems biology
Sabidó, E., Selevsek, N., & Aebersold, R. H. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.11.014 · Cited by 108 · see citing works
Peng, Y., Gregorich, Z. R., Valeja, S. G., Zhang, H., Cai, W., Chen, Y.-C., Guner, H., Chen, A. J., Schwahn, D. J., Hacker, T. A., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.040675 · Cited by 107 · see citing works
Self-citationAugmented Phosphorylation of Cardiac Troponin I in Hypertensive Heart Failure
Dong, X., Sumandea, C. A., Chen, Y.-C., Garcia-Cazarin, M. L., Zhang, J., Balke, C. W., Sumandea, M. P., & Ge, Y. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.293258 · Cited by 99 · see citing works
Self-citationMuneeruddin, K., Nazzaro, M., & Kaltashov, I. A. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b02982 · Cited by 98 · see citing works
Karabacak, M., Li, L., Tiwari, A., Hayward, L. J., Hong, P., Easterling, M. L., & Agar, J. N. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800099-mcp200 · Cited by 95 · see citing works
Top-down quantitation and characterization of SILAC-labeled proteins
Waanders, L. F., Hanke, S., & Mann, M. (2007) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2007.09.001 · Cited by 94 · see citing works
Definition of the mitochondrial proteome by measurement of molecular masses of membrane proteins
Carroll, J., Fearnley, I., & Walker, J. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0607719103 · Cited by 92 · see citing works
Mazur, M. T., Cardasis, H. L., Spellman, D. S., Liaw, A., Yates, N. A., & Hendrickson, R. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910776107 · Cited by 87 · see citing works
In-Spray Supercharging of Peptides and Proteins in Electrospray Ionization Mass Spectrometry
Miladinović, S. M., Fornelli, L., Lu, Y., Piech, K. M., Girault, H. H., & Tsybin, Y. O. (2012) · Analytical Chemistry · doi:10.1021/ac300845n · Cited by 87 · see citing works
Ayaz‐Güner, Ş., Zhang, J., Li, L., Walker, J. W., & Ge, Y. (2009) · Biochemistry · doi:10.1021/bi900739f · Cited by 87 · see citing works
Self-citationModulation of Thin Filament Activation by Breakdown or Isoform Switching of Thin Filament Proteins
Marston, S. B., & Redwood, C. S. (2003) · Circulation Research · doi:10.1161/01.res.0000105088.06696.17 · Cited by 86 · see citing works
Sterling, H. J., Batchelor, J. D., Wemmer, D. E., & Williams, E. R. (2010) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2010.02.003 · Cited by 85 · see citing works
New Mass-Spectrometry-Compatible Degradable Surfactant for Tissue Proteomics
Chang, Y.-H., Gregorich, Z. R., Chen, A. J., Hwang, L., Guner, H., Yu, D., Zhang, J., & Ge, Y. (2015) · Journal of Proteome Research · doi:10.1021/pr5012679 · Cited by 80 · see citing works
Self-citationInterpreting Top-Down Mass Spectra Using Spectral Alignment
Frank, A. M., Pesavento, J. J., Mizzen, C. A., Kelleher, N. L., & Pevzner, P. A. (2008) · Analytical Chemistry · doi:10.1021/ac702324u · Cited by 77 · see citing works
Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry.
Sharma, S., Simpson, D., Toliċ, N., Jaitly, N., Mayampurath, A., Smith, R. D., & Paša-Tolić, L. (2007) · Journal of Proteome Research · doi:10.1021/pr060354a · Cited by 77 · see citing works
Valeja, S. G., Xiu, L., Gregorich, Z. R., Güner, H., Jin, S., & Ge, Y. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00657 · Cited by 77 · see citing works
Self-citationTop Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions
Catherman, A. D., Li, M., Tran, J. C., Durbin, K. R., Compton, P. D., Early, B. P., Thomas, P. M., & Kelleher, N. L. (2013) · Analytical Chemistry · doi:10.1021/ac3031527 · Cited by 76 · see citing works
Du, Y., Parks, B. A., Sohn, S., Kwast, K. E., & Kelleher, N. L. (2005) · Analytical Chemistry · doi:10.1021/ac050993p · Cited by 76 · see citing works
New Insights into the p38 γ and p38 δ MAPK Pathways
Risco, A., & Cuenda, A. (2011) · Journal of Signal Transduction · doi:10.1155/2012/520289 · Cited by 70 · see citing works
Proteomics in heart failure: top-down or bottom-up?
Gregorich, Z. R., Chang, Y.-H., & Ge, Y. (2014) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-014-1471-9 · Cited by 69 · see citing works
Self-citationXiu, L., Valeja, S. G., Alpert, A. J., Jin, S., & Ge, Y. (2014) · Analytical Chemistry · doi:10.1021/ac501836k · Cited by 68 · see citing works
Self-citationValeja, S. G., Kaiser, N. K., Xian, F., Hendrickson, C. L., Rouse, J. C., & Marshall, A. G. (2011) · Analytical Chemistry · doi:10.1021/ac202429c · Cited by 67 · see citing works
Zhang, J., Dong, X., Hacker, T. A., & Ge, Y. (2010) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2010.02.005 · Cited by 66 · see citing works
Self-citationWhy does troponin I have so many phosphorylation sites? Fact and fancy
Solaro, R. J., & van der Velden, J. (2010) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2010.02.014 · Cited by 66 · see citing works
de Tombe, P. P., & Solaro, R. J. (2000) · Annals of Biomedical Engineering · doi:10.1114/1.1312189 · Cited by 61 · see citing works
Chen, X., Westphall, M. S., & Smith, L. M. (2003) · Analytical Chemistry · doi:10.1021/ac030127h · Cited by 54 · see citing works
Solis, R. S., Ge, Y., & Walker, J. W. (2008) · Journal of Muscle Research and Cell Motility · doi:10.1007/s10974-009-9168-y · Cited by 50 · see citing works
Self-citationKostyukevich, Y., Vladimirov, G., & Николаев, Е. Н. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0480-1 · Cited by 50 · see citing works
Intact proteome fractionation strategies compatible with mass spectrometry
Doucette, A. A., Tran, J. C., Wall, M. J., & Fitzsimmons, S. (2011) · Expert Review of Proteomics · doi:10.1586/epr.11.67 · Cited by 50 · see citing works
A Mechanical Nanomembrane Detector for Time-of-Flight Mass Spectrometry
Park, J., Qin, H., Scalf, M., Hilger, R. T., Westphall, M. S., Smith, L. M., & Blick, R. H. (2011) · Nano Letters · doi:10.1021/nl201645u · Cited by 44 · see citing works
Top-down Targeted Proteomics for Deep Sequencing of Tropomyosin Isoforms
Peng, Y., Chen, X., Zhang, H., Xu, Q., Hacker, T. A., & Ge, Y. (2012) · Journal of Proteome Research · doi:10.1021/pr301054n · Cited by 44 · see citing works
Self-citationIn-depth proteomic analysis of human tropomyosin by top-down mass spectrometry
Peng, Y., Yu, D., Gregorich, Z., Chen, X., Beyer, A. M., Gutterman, D. D., & Ge, Y. (2013) · Journal of Muscle Research and Cell Motility · doi:10.1007/s10974-013-9352-y · Cited by 42 · see citing works
Self-citationWang, Y., Pinto, J. R., Solis, R. S., Dweck, D., Liang, J., Diaz-Perez, Z., Ge, Y., Walker, J. W., & Potter, J. D. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.294306 · Cited by 41 · see citing works
Self-citationSouda, P., Ryan, C. M., Cramer, W. A., & Whitelegge, J. P. (2011) · Methods · doi:10.1016/j.ymeth.2011.09.019 · Cited by 38 · see citing works
Bergmann, U., Ahrends, R., Neumann, B., Scheler, C., & Linscheid, M. W. (2012) · Analytical Chemistry · doi:10.1021/ac203460b · Cited by 36 · see citing works
Drake, T. A., & Ping, P. (2006) · Journal of Lipid Research · doi:10.1194/jlr.r600027-jlr200 · Cited by 34 · see citing works
HPLC and Mass Spectrometry of Intrinsic Membrane Proteins
Whitelegge, J. P. (2004) · Humana Press eBooks · doi:10.1385/1-59259-742-4:323 · Cited by 33 · see citing works
Ultrahigh pressure fast size exclusion chromatography for top‐down proteomics
Chen, X., & Ge, Y. (2013) · PROTEOMICS · doi:10.1002/pmic.201200594 · Cited by 33 · see citing works
Self-citationMyosin Binding Protein C in the Heart
de Tombe, P. P. (2006) · Circulation Research · doi:10.1161/01.res.0000225873.63162.c4 · Cited by 33 · see citing works
Effective Top-Down LC/MS+ Method for Assessing Actin Isoforms as a Potential Cardiac Disease Marker
Chen, Y.-C., Ayaz-Guner, S., Peng, Y., Lane, N. M., Locher, M. R., Kohmoto, T., Larsson, L., Moss, R. L., & Ge, Y. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b01745 · Cited by 31 · see citing works
Self-citationScherperel, G., & Reid, G. E. (2007) · The Analyst · doi:10.1039/b618499p · Cited by 30 · see citing works
Top‐down mass spectrometry of cardiac myofilament proteins in health and disease
Peng, Y., Ayaz‐Güner, Ş., Yu, D., & Ge, Y. (2014) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201400043 · Cited by 29 · see citing works
Self-citationGregorich, Z. R., Peng, Y., Lane, N. M., Wolff, J. J., Wang, S., Guo, W., Güner, H., Doop, J., Hacker, T. A., & Ge, Y. (2015) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2015.08.007 · Cited by 27 · see citing works
Self-citationCopeland, O., Nowak, K. J., Laing, N. G., Ravenscroft, G., Messer, A. E., Bayliss, C. R., & Marston, S. B. (2010) · Journal of Muscle Research and Cell Motility · doi:10.1007/s10974-010-9224-7 · Cited by 26 · see citing works
Intact protein mass spectrometry and top-down proteomics
Whitelegge, J. P. (2013) · Expert Review of Proteomics · doi:10.1586/epr.13.10 · Cited by 24 · see citing works
Huang, T., & McLuckey, S. A. (2010) · PROTEOMICS · doi:10.1002/pmic.201000187 · Cited by 21 · see citing works
Size Exclusion High-Performance Liquid Chromatography of Small Solutes
Alpert, A. J. (1999) · Elsevier eBooks · doi:10.1016/b978-012765555-0/50009-9 · Cited by 15 · see citing works
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- [64]Tran JC Zamdborg L Ahlf DR Mapping intact protein isoforms in discovery mode using top-down proteomics Nature 2011 480 254 8 22037311 PMC3237778
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Gao, L., Gregorich, Z. R., Zhu, W., Mattapally, S., Oduk, Y., Lou, X., Kannappan, R., Borovjagin, A. V., Walcott, G. P., Pollard, A. E., et al. (2017) · Circulation · doi:10.1161/circulationaha.117.030785 · Cited by 465 · see citing works
Self-citationHigh-throughput proteomics: a methodological mini-review
Cui, M., Cheng, C., & Zhang, L. (2022) · Laboratory Investigation · doi:10.1038/s41374-022-00830-7 · Cited by 375 · see citing works
Top-Down Proteomics: Ready for Prime Time?
Chen, B., Brown, K. A., Lin, Z., & Ge, Y. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04747 · Cited by 210 · see citing works
Self-citationIdentification and Quantification of Proteoforms by Mass Spectrometry
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., et al. (2019) · PROTEOMICS · doi:10.1002/pmic.201800361 · Cited by 209 · see citing works
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Melby, J. A., Roberts, D. S., Larson, E. J., Brown, K. A., Bayne, E. F., Jin, S., & Ge, Y. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00099 · Cited by 191 · see citing works
Self-citationTop-down proteomics: challenges, innovations, and applications in basic and clinical research
Brown, K. A., Melby, J. A., Roberts, D. S., & Ge, Y. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1855982 · Cited by 152 · see citing works
Self-citationRoberts, 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. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00318-2 · Cited by 154 · see citing works
Self-citationCai, W., Tucholski, T., Chen, B., Alpert, A. J., McIlwain, S., Kohmoto, T., Jin, S., & Ge, Y. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00380 · Cited by 135 · see citing works
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Brown, K. A., Chen, B., Guardado-Alvarez, T. M., Lin, Z., Hwang, L., Ayaz-Guner, S., Jin, S., & Ge, Y. (2019) · Nature Methods · doi:10.1038/s41592-019-0391-1 · Cited by 111 · see citing works
Self-citationTucholski, T., Cai, W., Gregorich, Z. R., Bayne, E. F., Mitchell, S. D., McIlwain, S. J., de Lange, W. J., Wrobbel, M., Karp, H., Hite, Z., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006764117 · Cited by 107 · see citing works
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Cai, W., Zhang, J., de Lange, W. J., Gregorich, Z. R., Karp, H., Farrell, E. T., Mitchell, S. D., Tucholski, T., Lin, Z., Biermann, M., et al. (2019) · Circulation Research · doi:10.1161/circresaha.119.315305 · Cited by 78 · see citing works
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Brown, K. A., Tucholski, T., Alpert, A. J., Eken, C., Wesemann, L., Kyrvasilis, A., Jin, S., & Ge, Y. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c02533 · Cited by 35 · see citing works
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Lin, Z., Wei, L., Cai, W., Zhu, Y., Tucholski, T., Mitchell, S. D., Guo, W., Ford, S. P., Diffee, G. M., & Ge, Y. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.001086 · Cited by 36 · see citing works
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Wang, H., & Tian, Z. (2018) · Journal of Chromatography A · doi:10.1016/j.chroma.2018.06.013 · Cited by 30 · see citing works
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McIlwain, S. J., Wu, Z., Wetzel, M., Belongia, D., Jin, Y., Wenger, K., Ong, I. M., & Ge, Y. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00035 · Cited by 27 · see citing works
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Borgmann-Winter, K., Wang, K., Bandyopadhyay, S., Torshizi, A. D., Blair, I., & Hahn, C. (2019) · Schizophrenia Research · doi:10.1016/j.schres.2019.07.025 · Cited by 20 · see citing works
Melby, J. A., Jin, Y., Lin, Z., Tucholski, T., Wu, Z., Gregorich, Z. R., Diffee, G. M., & Ge, Y. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00623 · Cited by 20 · see citing works
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Cai, W., Hite, Z., Lyu, B., Wu, Z., Lin, Z.-Q., Gregorich, Z., Messer, A., McIlwain, S., Marston, S. B., Kohmoto, T., et al. (2018) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2018.07.247 · Cited by 18 · see citing works
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Lin, Z.-Q., Guo, F., Gregorich, Z., Sun, R.-X., Zhang, H., Hu, Y., Shanmuganayagam, D., & Ge, Y. (2018) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-018-1925-y · Cited by 15 · see citing works
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Schaffer, L. V., Tucholski, T., Shortreed, M. R., Ge, Y., & Smith, L. M. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02343 · Cited by 17 · see citing works
Self-citationHorita, H. N., Law, A., & Middleton, K. M. (2018) · Proteomes · doi:10.3390/proteomes6020024 · Cited by 17 · see citing works
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Self-citationBayne, E. F., Rossler, K. J., Gregorich, Z., Aballo, T. J., Roberts, D. S., Chapman, E. A., Guo, W., Palecek, S., Ralphe, J., Kamp, T., et al. (2023) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2023.06.003 · Cited by 14 · see citing works
Self-citationWang, X., Liu, X., Li, L., Zhang, F., Hu, M. Q., Ren, F., Chi, L., & Linhardt, R. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0167727 · Cited by 16 · see citing works
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Guang, X., Stupak, J., Li, Y., Hu, L., Guo, B., & Li, J. (2018) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.8103 · Cited by 16 · see citing works
Plymire, D. A., Wing, C. E., Robinson, D. E., & Patrie, S. M. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02426 · Cited by 15 · see citing works
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Brown, K. A., Tucholski, T., Eken, C., Knott, S., Zhu, Y., Jin, S., & Ge, Y. (2020) · Angewandte Chemie · doi:10.1002/ange.201915374 · Cited by 14 · see citing works
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Cai, F., Gu, Y., Ling, Y., Yi, G., Zang, S., Su, T., Liu, Y., Li, A., Wang, D., Zhao, W., et al. (2025) · Biomarker Research · doi:10.1186/s40364-025-00805-y · Cited by 14 · see citing works
Wang, H., & Tian, Z. (2018) · Journal of Separation Science · doi:10.1002/jssc.201800689 · Cited by 14 · see citing works
Toward the analysis of functional proteoforms using mass spectrometry-based stability proteomics
Kang, J., Seshadri, M., Cupp‐Sutton, K. A., & Wu, S. (2023) · Frontiers in Analytical Science · doi:10.3389/frans.2023.1186623 · Cited by 14 · see citing works
Mann, M. W., Fu, Y., Gearhart, R. L., Xu, X., Roberts, D. S., Li, Y., Zhou, J., Ge, Y., & Brasier, A. R. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1212770 · Cited by 16 · see citing works
Self-citationThe Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective
Chen, B., Guo, X. Q., Tucholski, T., Lin, Z., McIlwain, S. J., & Ge, Y. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1710-3 · Cited by 14 · see citing works
Self-citationThe Human Proteoform Project: A Plan to Define the Human ProteomePreprint
Smith, L. M., Agar, J. N., Chamot‐Rooke, J., Danis, P. O., Ge, Y., Loo, J. A., Paša‐Tolić, L., Tsybin, Y. O., & Kelleher, N. L. (2020) · Preprints.org · doi:10.20944/preprints202010.0368.v1 · Cited by 16 · see citing works
Self-citationRamírez‐Sagredo, A., Sunny, A. T., Cupp‐Sutton, K. A., Chowdhury, T., Zhao, Z., Wu, S., & Chiao, Y. A. (2024) · Clinical Proteomics · doi:10.1186/s12014-024-09509-1 · Cited by 14 · see citing works
Wu, Z., Jin, Y., Chen, B., Gugger, M. K., Wilkinson-Johnson, C. L., Tiambeng, T. N., Jin, S., & Ge, Y. (2019) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-019-02341-0 · Cited by 13 · see citing works
Self-citationWang, B., Fields, L., & Li, L.-J. (2022) · Proteomics · doi:10.1002/pmic.202200286 · Cited by 8 · see citing works
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Mann, M. W., & Brasier, A. R. (2021) · Expert Review of Proteomics · doi:10.1080/14789450.2021.1931130 · Cited by 8 · see citing works
Zhang, M., Wang, H., Bhandari, R., Pan, Q., & Sun, F. (2021) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-021-03215-9 · Cited by 9 · see citing works
Psatha, K., Kollipara, L., Voutyraki, C., Divanach, P., Sickmann, A., Rassidakis, G. Z., Drakos, E., & Aivaliotis, M. (2016) · Journal of Chromatography B · doi:10.1016/j.jchromb.2016.11.005 · Cited by 8 · see citing works
SPECTRUM – A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data
Basharat, A. R., Iman, K., Khalid, M. F., Anwar, Z., Hussain, R., Kabir, H., Tahreem, M., Shahid, A., Humayun, M., Hayat, H. A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-47724-1 · Cited by 7 · see citing works
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Liu, L., Yang, T., Jiang, Q., Sun, J., Gu, L., Wang, S., Li, Y., Chen, B., Zhao, D., Sun, R., et al. (2022) · Biomolecules and Biomedicine · doi:10.17305/bjbms.2022.7770 · Cited by 7 · see citing works
Sagu, S. T., Rawel, H. M., & Rohn, S. (2022) · Molecules · doi:10.3390/molecules27185834 · Cited by 7 · see citing works
SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD)
Quick, M. M., Mehaffey, M. R., Johns, R. W., Parker, W. R., & Brodbelt, J. S. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1650-y · Cited by 7 · see citing works
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Smith, B. J., & Martins‐de‐Souza, D. (2021) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-77252-9_2 · Cited by 7 · see citing works
Recent Advancements and Applications of Size Exclusion Chromatography in Modern Analysis
Bhatia, R., Kumari, Y., & Chopra, A. (2023) · Current Analytical Chemistry · doi:10.2174/1573411019666230526144816 · Cited by 6 · see citing works
Gao, Z., Rossler, K. J., Rogers, H. T., Gregorich, Z. R., Aballo, T. J., Chapman, E. A., Price, S. J., Hermsen, J. L., de Lange, W. J., Zhu, Y., et al. (2025) · Circulation Heart Failure · doi:10.1161/circheartfailure.125.012899 · Cited by 6 · see citing works
Self-citationPatrie, S. M., & Cline, E. N. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-818607-7.00017-7 · Cited by 5 · see citing works
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Nimer, R. M., & Rahman, A. M. A. (2023) · Expert Review of Proteomics · doi:10.1080/14789450.2023.2258282 · Cited by 4 · see citing works
Yue, Y.-F., Fang, F., Gao, G., Sadeghi, S., Colón-Rosado, J. A., Nimavard, R. T., Askarani, M. F., Thorp, L., Dashtaki, M. R., Zhu, G., et al. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c01194 · Cited by 2 · see citing works
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Shang, L., Wang, W., Liu, Y., Tang, B., & Hou, Y. (2025) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.70760 · Cited by 4 · see citing works
Deconvolving Native and Intact Protein Mass Spectra with UniDec.Preprint
Kostelic, M. M., & Marty, M. (2020) · Methods in molecular biology · doi:10.26434/chemrxiv.13417118.v1 · Cited by 18 · see citing works
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Zhan, X. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.83687 · Cited by 2 · see citing works
iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm
Chang, H.-Y., Chen, C.-T., Ko, C.-L., Chen, Y., Chen, Y., Hsu, W., Juo, C., & Sung, T. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02343 · Cited by 2 · see citing works
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Hoff, F. W., van Dijk, A. D., & Kornblau, S. M. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.90329 · Cited by 2 · see citing works
Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective
Balli, O. I., Uversky, V., Durdağı, S., & Coskuner-Weber, O. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26242 · Cited by 1 · see citing works
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Blackler, A. R., & Duncan, M. W. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-813539-6.00009-2 · Cited by 2 · see citing works
Mann, M. W., Fu, Y., Xu, X., Roberts, D. S., Li, Y., Zhou, J., Ge, Y., & Brasier, A. (2023) · bioRxiv · doi:10.1101/2023.01.17.524257 · Cited by 1 · see citing works
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O’Reilly, J., Lindsey, M. L., & Baugh, J. A. (2017) · Current Opinion in Physiology · doi:10.1016/j.cophys.2017.12.010 · Cited by 1 · see citing works
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Araújo, J. D. S., & Machado, O. L. T. (2019) · Proteoforms - Concept and Applications in Medical Sciences · doi:10.5772/intechopen.89914 · Cited by 1 · see citing works
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Kostelic, M. M., & Marty, M. T. (2020) · ChemRxiv · doi:10.26434/chemrxiv.13417118 · Cited by 1 · see citing works
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Safaei, A., & Oskouie, A. A. (2018) · Translational bioinformatics · doi:10.1007/978-981-10-8764-6_6
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Lin, Z., 黎明威, 文轩蔡, 燕龙朱, Tucholski, T., Mitchell., 斯., 魏国, Ford., 斯., Defree, G. M., & Ge, Y. (2019)
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Mezger, S. T. P. (2022) · doi:10.26481/dis.20220712sm
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Schaffer, L. V., Shortreed, M. R., & Smith, L. M. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2325-1_7
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Yu, J., Kim, M.-J., & Park, H.-M. (2023) · KSBB Journal · doi:10.7841/ksbbj.2023.38.1.12
Yin, X., & Mayr, M. (2025) · Cardiovascular Research · doi:10.1093/cvr/cvaf103
- Authors
- Cai, W., Tucholski, T. M., Gregorich, Z. R., & Ge, Y.
- Affiliations
- University of Wisconsin–Madison (US)
- Corresponding author
- Ge, Ying
- Venue
- Expert Review of Proteomics
- Publisher
- Informa UK Limited
- Published
- 2016-07-26
- Volume
- 13
- Issue
- 8
- Pages
- 717-730
- ISSN
- 1478-9450 (ISSN-L)
- 1744-8387
- PMC
- PMC5026638
- OpenAlex
- W2475449079
- Cited by
- 99
- References
- 104
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 3 · 2023: 10 · 2022: 9 · 2021: 10 · 2020: 15 · 2019: 18 · 2018: 14 · 2017: 11 · 2016: 3
- FWCI
- 1.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Expert Review of Proteomics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (NIH R01HL096971 and R01HL109810)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- top-down proteomics, heart disease, cardiac proteome, post-translational modification, protein isoforms, high-resolution mass spectrometry, biomarkers, therapeutic target
- MeSH terms
- Heart Diseases, Humans, Protein Processing, Post-Translational, Mass Spectrometry, Biomarkers, Protein Isoforms, Proteome, Proteomics
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