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Top Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions

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Top-Down Approaches for Measuring Expression Ratios of Intact Yeast Proteins Using Fourier Transform Mass Spectrometry

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 Reagents for Enhanced Liquid Chromatographic Separation and Charging of Intact Protein Ions for Electrospray Ionization Mass Spectrometry

Valeja, S. G., Tipton, J. D., Emmett, M. R., & Marshall, A. G. (2010) · Analytical Chemistry · doi:10.1021/ac1016858 · Cited by 76 · see citing works

S100A7, a Novel Alzheimer's Disease Biomarker with Non-Amyloidogenic α-Secretase Activity Acts via Selective Promotion of ADAM-10

Qin, W., Ho, L., Wang, J., Peskind, E. R., & Pasinetti, G. M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004183 · Cited by 75 · see citing works

Top-Down Proteomics and Direct Surface Sampling of Neonatal Dried Blood Spots: Diagnosis of Unknown Hemoglobin Variants

Edwards, R., Griffiths, P., Bunch, J., & Cooper, H. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0477-9 · Cited by 75 · see citing works

Molecular and Integrated Biology of Thin Filament Protein Phosphorylation in Heart Muscle

Sumandea, M. P., Burkart, E. M., Kobayashi, T., de Tombe, P. P., & Solaro, R. J. (2004) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1302.004 · Cited by 75 · see citing works

Top-Down Identification and Quantification of Stable Isotope Labeled Proteins from Aspergillus flavus Using Online Nano-Flow Reversed-Phase Liquid Chromatography Coupled to a LTQ-FTICR Mass Spectrometer

Collier, T. S., Hawkridge, A. M., Georgianna, D. R., Payne, G. A., & Muddiman, D. C. (2008) · Analytical Chemistry · doi:10.1021/ac800254z · Cited by 74 · see citing works

MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization

Guner, H., Close, P. L., Cai, W., Zhang, H., Peng, Y., Gregorich, Z. R., & Ge, Y. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-013-0789-4 · Cited by 73 · see citing works

Novel mass spectrometric immunoassays for the rapid structural characterization of plasma apolipoproteins

Niederkofler, E. E., Tubbs, K. A., Kiernan, U. A., Nedelkov, D., & Nelson, R. W. (2003) · Journal of Lipid Research · doi:10.1194/jlr.d200034-jlr200 · Cited by 71 · see citing works

A Common Property of Amyotrophic Lateral Sclerosis-associated Variants

Molnar, K. S., Karabacak, M., Johnson, J. L., Wang, Q., Tiwari, A., Hayward, L. J., Coales, S. J., Hamuro, Y., & Agar, J. N. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.023945 · Cited by 71 · see citing works

Unit Mass Baseline Resolution for an Intact 148 kDa Therapeutic Monoclonal Antibody by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Valeja, 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

Deciphering modifications in swine cardiac troponin I by top-down high-resolution tandem mass spectrometry

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

Quantitative top-down proteomics of SILAC labeled human embryonic stem cells

Collier, T. S., Sarkar, P., Rao, B. M., & Muddiman, D. C. (2010) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2010.01.031 · Cited by 66 · see citing works

Differential expression of histone post-translational modifications in acute myeloid and chronic lymphocytic leukemia determined by high-pressure liquid chromatography and mass spectrometry

Zhang, L., Freitas, M. A., Wickham, J., Parthun, M. R., Klisovic, M. I., Marcucci, G., & Byrd, J. C. (2003) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2003.10.001 · Cited by 63 · see citing works

Precursor ion independent algorithm for top-down shotgun proteomics

Tsai, Y. S., Scherl, A., Shaw, J. L., Mackay, C. L., Shaffer, S. A., Langridge‐Smith, P. R. R., & Goodlett, D. R. (2009) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2009.07.024 · Cited by 59 · see citing works

Using size exclusion chromatography‐RPLC and RPLC‐CIEF as two‐dimensional separation strategies for protein profiling

Simpson, D. C., Ahn, S., Paša‐Tolić, L., Bogdanov, B., Mottaz, H. M., Vilkov, A. N., Anderson, G., Lipton, M. S. W., & Smith, R. D. (2006) · Electrophoresis · doi:10.1002/elps.200600037 · Cited by 57 · see citing works

Mass Spectrometric Analysis of DNA Mixtures: Instrumental Effects Responsible for Decreased Sensitivity with Increasing Mass

Chen, X., Westphall, M. S., & Smith, L. M. (2003) · Analytical Chemistry · doi:10.1021/ac030127h · Cited by 54 · see citing works

Single amino acid sequence polymorphisms in rat cardiac troponin revealed by top–down tandem mass spectrometry

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

Dynamically Harmonized FT-ICR Cell with Specially Shaped Electrodes for Compensation of Inhomogeneity of the Magnetic Field. Computer Simulations of the Electric Field and Ion Motion Dynamics

Kostyukevich, 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

Analysis of Human C1q by Combined Bottom-up and Top-down Mass Spectrometry

Pflieger, D., Przybylski, C., Gonnet, F., Caër, J. L., Lunardi, T., Arlaud, G. J., & Daniel, R. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900350-mcp200 · Cited by 47 · see citing works

Detection of Genetic Variants of Transthyretin by Liquid Chromatography–Dual Electrospray Ionization Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry

Nepomuceno, A. I., Mason, C. J., Muddiman, D. C., Bergen, H. R., & Zeldenrust, S. R. (2004) · Clinical Chemistry · doi:10.1373/clinchem.2004.033274 · Cited by 46 · 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

Top-down analysis of small plasma proteins using an LTQ-Orbitrap. Potential for mass spectrometry-based clinical assays for transthyretin and hemoglobin

Théberge, R., Infusini, G., Tong, W., McComb, M. E., & Costello, C. E. (2010) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2010.08.012 · Cited by 44 · see citing works

Post-Translational Modification by Cysteine Protects Cu/Zn-Superoxide Dismutase from Oxidative Damage

Auclair, J. R., Johnson, J. L., Liu, Q., et al. (2013) · Biochemistry · doi:10.1021/bi4006122 · Cited by 42 · see citing works

Significant Modifications of the Salivary Proteome Potentially Associated with Complications of Down Syndrome Revealed by Top-down Proteomics

Cabras, T., Pisano, E., Montaldo, C., Giuca, M. R., Iavarone, F., Zampino, G., Castagnola, M., & Messana, I. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.026708 · Cited by 42 · see citing works

Cerebrospinal fluid top‐down proteomics evidenced the potential biomarker role of LVV ‐ and VV ‐hemorphin‐7 in posterior cranial fossa pediatric brain tumors

Desiderio, C., D’Angelo, L., Rossetti, D. V., Iavarone, F., Giardina, B., Castagnola, M., Massimi, L., Tamburrini, G., & Rocco, C. D. (2012) · PROTEOMICS · doi:10.1002/pmic.201100499 · Cited by 40 · see citing works

High Resolution Electron Transfer Dissociation Studies of Unfractionated Intact Histones from Murine Embryonic Stem Cells Using On-line Capillary LC Separation

Eliuk, S. M., Maltby, D. A., Panning, B., & Burlingame, A. L. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900569-mcp200 · Cited by 37 · see citing works

Role of Troponin I Phosphorylation in Protein Kinase C-mediated Enhanced Contractile Performance of Rat Myocytes

Westfall, M. V., & Borton, A. R. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305404200 · Cited by 36 · see citing works

Application of Metal-Coded Affinity Tags (MeCAT): Absolute Protein Quantification with Top-Down and Bottom-Up Workflows by Metal-Coded Tagging

Bergmann, U., Ahrends, R., Neumann, B., Scheler, C., & Linscheid, M. W. (2012) · Analytical Chemistry · doi:10.1021/ac203460b · Cited by 36 · see citing works

Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Proteomics approaches to the systems biology of cardiovascular diseases

Drake, T. A., & Ping, P. (2006) · Journal of Lipid Research · doi:10.1194/jlr.r600027-jlr200 · Cited by 34 · see citing works

Mass Spectrometry as an Emerging Tool for Systems Biology

Yates, J. R. (2004) · BioTechniques · doi:10.2144/04366te01 · 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

Proteomics: biology in the post‐genomic era

Brower, V. (2001) · EMBO Reports · doi:10.1093/embo-reports/kve144 · Cited by 28 · see citing works

Building Multidimensional Biomarker Views of Type 2 Diabetes on the Basis of Protein Microheterogeneity

Borges, C. R., Oran, P. E., Buddi, S. P., Jarvis, J. W., Schaab, M. R., Rehder, D. S., Rogers, S. P., Taylor, T. J. S., & Nelson, R. W. (2011) · Clinical Chemistry · doi:10.1373/clinchem.2010.156976 · Cited by 27 · see citing works

Electron Transfer Dissociation Mass Spectrometry of Hemoglobin on Clinical Samples

Graça, D. C., Lescuyer, P., Clerici, L., et al. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0446-3 · Cited by 25 · 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

Tearing the Top Off ‘Top-Down’ Proteomics

Perkel, J. M. (2012) · BioTechniques · doi:10.2144/000113900 · Cited by 5 · see citing works

Identification 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

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

Top-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

Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy

Cai, 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

MASH 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 &amp; Cellular Proteomics · doi:10.1074/mcp.o115.054387 · Cited by 132 · see citing works

An RNA-Seq atlas of gene expression in mouse and rat normal tissues

Söllner, J. F., Leparc, G., Hildebrandt, T., Klein, H., Thomas, L., Stupka, E., & Simon, E. (2017) · Scientific Data · doi:10.1038/sdata.2017.185 · Cited by 133 · 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

Top-down Proteomics Reveals Concerted Reductions in Myofilament and Z-disc Protein Phosphorylation after Acute Myocardial Infarction

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 &amp; Cellular Proteomics · doi:10.1074/mcp.m114.040675 · Cited by 107 · see citing works

Top-down Proteomics: Technology Advancements and Applications to Heart Diseases

Cai, W., Tucholski, T. M., Gregorich, Z. R., & Ge, Y. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2016.1209414 · Cited by 99 · see citing works

High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer

Cleland, T. P., DeHart, C. J., Fellers, R. T., VanNispen, A. J., Greer, J. B., LeDuc, R. D., Parker, W. R., Thomas, P. M., Kelleher, N. L., & Brodbelt, J. S. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00043 · Cited by 96 · 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

pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification

Sun, R.-X., Luo, L., Wu, L., Wang, R.-M., Zeng, W.-F., Chi, H., Liu, C., & He, S.-M. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03963 · Cited by 71 · see citing works

Coupling Capillary Zone Electrophoresis with Electron Transfer Dissociation and Activated Ion Electron Transfer Dissociation for Top-Down Proteomics

Zhao, Y., Riley, N. M., Sun, L., Hebert, A. S., Yan, X., Westphall, M. S., Rush, M. J. P., Zhu, G., Champion, M. M., Medie, F. M., et al. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00883 · Cited by 55 · see citing works

Novel Sarcopenia-related Alterations in Sarcomeric Protein Post-translational Modifications (PTMs) in Skeletal Muscles Identified by Top-down Proteomics

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., et al. (2018) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.ra117.000124 · Cited by 47 · see citing works

Coupling functionalized cobalt ferrite nanoparticle enrichment with online LC/MS/MS for top-down phosphoproteomics

Chen, B., Hwang, L., Ochowicz, W., Lin, Z., Guardado-Alvarez, T. M., Cai, W., Xiu, L., Dani, K., Colah, C., Jin, S., et al. (2017) · Chemical Science · doi:10.1039/c6sc05435h · Cited by 43 · see citing works

Middle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation

Chen, B., Lin, Z., Zhu, Y., Jin, Y., Larson, E., Xu, Q., Fu, C., Zhang, Z., Zhang, Q., Pritts, W. A., et al. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02194 · Cited by 38 · see citing works

The benefits (and misfortunes) of SDS in top-down proteomics

Kachuk, C., & Doucette, A. A. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2017.03.002 · Cited by 39 · 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

Top-Down Proteomics Reveals Myofilament Proteoform Heterogeneity among Various Rat Skeletal Muscle Tissues

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

A high-stringency blueprint of the human proteome

Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210 · see citing works

The human eye proteome project

Omenn, G. S. (2013) · PROTEOMICS · doi:10.1002/pmic.201300255 · Cited by 9 · see citing works

Mouse models for neurodegenerative diseases and a theory of proteomics

Klose, J. (2003) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.85.s2.8_1.x

Human Proteome Project and Current Bioinformatics Status in Disease Diagnosis and Treatment

Anwar, P., Javed, A., Amjad, I., Arif, I., Sadiqa, A., Akram, H., & Azhar, L. (2018) · Journal of Proteomics and Genomics research · doi:10.14302/issn.2326-0793.jpgr-18-2004 · Cited by 1 · see citing works

Cancer proteome-expression database: Genome Medicine Database of Japan Proteomics

Kondo, T. (2010) · Expert Review of Proteomics · doi:10.1586/epr.09.87 · Cited by 13 · see citing works