Top-Down Proteomics: Ready for Prime Time?

Chen, Bifan; Brown, Kyle A.; Lin, Ziqing; Ge, Ying

doi:10.1021/acs.analchem.7b04747

Cited by 210Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsAdvanced Biosensing Techniques and Applications

Top-Down Proteomics: Ready for Prime Time?

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Chen, Bifan, Brown, Kyle A., Lin, Ziqing, Ge, Ying·2018·Analytical Chemistry

DOI 10.1021/acs.analchem.7b04747PMC PMC6138622

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ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Top-Down Proteomics: Ready for Prime Time?Bifan ChenBifan ChenDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United StatesMore by Bifan ChenView Biographyhttp://orcid.org/0000-0003-0379-0821, Kyle A. BrownKyle A. BrownDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United StatesMore by Kyle A. BrownView Biography, Ziqing LinZiqing LinDepartment of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United StatesHuman Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United StatesMore by Ziqing LinView Biographyhttp://orcid.org/0000-0003-0464-5263, and Ying Ge*Ying GeDepartment of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United StatesDepartment of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United StatesHuman Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States*E-mail: [email protected]More by Ying GeView Biographyhttp://orcid.org/0000-0001-5211-6812Cite this: Anal. Chem. 2018, 90, 1, 110–127Publication Date (Web):November 21, 2017Publication History Published online21 November 2017Published inissue 2 January 2018https://pubs.acs.org/doi/10.1021/acs.analchem.7b04747https://doi.org/10.1021/acs.analchem.7b04747review-articleACS PublicationsCopyright © 2017 American Chemical SocietyRequest reuse permissionsArticle Views5168Altmetric-Citations153LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Fragmentation,Ions,Mass spectrometry,Peptides and proteins,Proteomics Get e-Alerts

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Top-down proteomics analyzes intact proteins and is preferred for unambiguous proteoform-resolved detail.
“For this reason, the “top-down” proteomics approach, which forgoes digestion to peptides and instead analyzes intact proteins, is the preferred method to achieve unambiguous, proteoform-resolved molecular detail (Figure 1) [15].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [15]
Protein solubility is a major challenge in top-down proteomics, especially for membrane proteins.
“One such challenge in top-down proteomics is protein solubility4, especially for membrane proteins, which comprise a large proportion of the proteome and play a critical role in many cellular functions and are important drug targets5,6.”
From A photocleavable surfactant for top-down proteomics (2019) · cites this paper as [4]
A major obstacle, particularly for newcomers, is the shortage of a general, easy-to-use program for streamlined analysis of complex top-down proteomics data, which restricts the field's broader impact.
“Particularly, the lack of a universal and user-friendly software for streamlined analysis of complex top-down proteomics data is becoming increasingly recognized as a major barrier, especially for newcomers, thus limiting the broader impact of top-down proteomics in the biomedical research communities.”
From MASH Explorer: A Universal Software Environment for Top-Down Proteomics (2020) · cites this paper as [7]
Software for analyzing protein-based top-down proteomics is still immature, largely because high-resolution intact protein mass spectra are extremely complex to handle.
“In contrast to the well-developed software packages in the peptide-based bottom-up proteomics, the data analysis tools for protein-based top-down proteomics remain under-developed due to the major challenge in handling the enormous complexity of high-resolution intact protein mass spectra.7–9”
From MASH Explorer: A Universal Software Environment for Top-Down Proteomics (2020) · cites this paper as [7]
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 [23]

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 [23]
Characterization of PTMs is of key importance for understanding cell signaling processes related to clinical disorders.
“Thus, characterization of PTMs is of key importance for understanding cell signaling processes related to clinical disorders16.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [16]
Top-down mass spectrometry is an emerging approach that provides detailed structural information on intact proteins, including PTM characterization.
“TDMS is an emerging approach that provides detailed structural information on intact proteins, including characterization of PTMs16.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [16]
Top-down analysis can provide unique structural insights into proteins through precise molecular weight measurements, identification of multiple PTMs, and in-depth proteoform characterization.
“Top-down analysis can provide unique insights into a protein’s structure by providing precise molecular weight measurements, the identification of multiple PTMs5,16,28 and in-depth proteoform characterization (different forms of a single protein generated from a gene)32.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [16]
PTM patterns can provide insight into potentially significant biological processes.
“PTM patterns can provide insight into potentially significant biological processes14,16,17”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [16]
Recent improvements in mass spectrometry instrumentation and bioinformatics have enabled TDMS to characterize and quantify hundreds to thousands of proteoforms in a single analysis.
“Recent improvements in mass spectrometry instrumentation and bioinformatics have enabled TDMS to be used to characterize and quantify hundreds to thousands of proteoforms in a single analysis16.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [16]
MS detection of low-abundance proteins from blood remains an unsolved challenge due to the extraordinary dynamic range of the blood proteome.
“However, the MS detection of low-abundance proteins remains an unsolved challenge due to high dynamic range of the human proteome8–10.”
From Nanoproteomics enables proteoform-resolved analysis of low-abundance proteins in human serum (2020) · cites this paper as [8]
Bottom-up protein analysis loses information regarding protein isoforms, PTM stoichiometry, and combinatorial PTMs.
“Information regarding protein isoforms, PTM stoichiometry, and combinatorial PTMs is, however, lost when using peptides as protein surrogates.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [13]
Top-down mass spectrometry is the premier MS-based technology for unambiguous proteoform characterisation, enabling in-depth sequencing, the discovery of novel proteoforms, and quantification of disease-associated PTMs.
“‘Top-down’ mass spectrometry, which forgoes the digestion step, has proven to be the premier MS-based technology for unambiguous proteoform characterisation, enabling in-depth sequencing, the discovery of novel proteoforms, and quantification of disease-associated PTMs.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [13]

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Savaryn, J. P., Catherman, A. D., Thomas, P. M., Abecassis, M. M., & Kelleher, N. L. (2013) · Genome Medicine · doi:10.1186/gm457 · Cited by 103 · see citing works
Applying Label-Free Quantitation to Top Down Proteomics
Ntai, I., Kim, K., Fellers, R. T., Skinner, O. S., Smith, A. D., Early, B. P., Savaryn, J. P., LeDuc, R. D., Thomas, P. M., & Kelleher, N. L. (2014) · Analytical Chemistry · doi:10.1021/ac500395k · Cited by 102 · see citing works
Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches
Petras, D., Heiss, P., Süßmuth, R. D., & Calvete, J. J. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00305 · Cited by 102 · see citing works
Augmented 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-citation
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
Self-citation
Characterization of Intact Protein Conjugates and Biopharmaceuticals Using Ion-Exchange Chromatography with Online Detection by Native Electrospray Ionization Mass Spectrometry and Top-Down Tandem Mass Spectrometry
Muneeruddin, K., Nazzaro, M., & Kaltashov, I. A. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b02982 · Cited by 98 · see citing works
Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry
Belov, A. M., Viner, R., Santos, M. R., Horn, D. M., Bern, M., Karger, B. L., & Ivanov, A. R. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1781-1 · Cited by 97 · 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
Characterization of Small Protein Aggregates and Oligomers Using Size Exclusion Chromatography with Online Detection by Native Electrospray Ionization Mass Spectrometry
Muneeruddin, K., Thomas, J. J., Salinas, P. A., & Kaltashov, I. A. (2014) · Analytical Chemistry · doi:10.1021/ac502590h · Cited by 96 · see citing works
Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry
Anderson, L. C., DeHart, C. J., Kaiser, N. K., Fellers, R. T., Smith, D. F., Greer, J. B., LeDuc, R. D., Blakney, G. T., Thomas, P. M., Kelleher, N. L., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00696 · Cited by 94 · see citing works
Size-Sorting Combined with Improved Nanocapillary-LC-MS for Identification of Intact Proteins up to 80 kDa
Vellaichamy, A., Tran, J. C., Catherman, A. D., Lee, J. E., Kellie, J. F., Sweet, S., Zamdborg, L., Thomas, P. M., Ahlf, D. R., Durbin, K. R., et al. (2010) · Analytical Chemistry · doi:10.1021/ac9021083 · Cited by 94 · see citing works
Advancements in Top-Down Proteomics
Zhou, H., Ning, Z., Starr, A. E., Abu‐Farha, M., & Figeys, D. (2011) · Analytical Chemistry · doi:10.1021/ac202882y · Cited by 94 · 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
High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-β1
Bush, D. R., Zang, L., Belov, A. M., Ivanov, A. R., & Karger, B. L. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03218 · Cited by 92 · 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
Exploring the Mechanism of Salt-Induced Signal Suppression in Protein Electrospray Mass Spectrometry Using Experiments and Molecular Dynamics Simulations
Metwally, H., McAllister, R. G., & Konermann, L. (2015) · Analytical Chemistry · doi:10.1021/ac5044016 · Cited by 92 · see citing works
Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics
Capriotti, A. L., Cavaliere, C., Foglia, P., Samperi, R., & Laganà, A. (2011) · Journal of Chromatography A · doi:10.1016/j.chroma.2011.05.094 · Cited by 91 · see citing works
Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer
Fornelli, L., Durbin, K. R., Fellers, R. T., Early, B. P., Greer, J. B., LeDuc, R. D., Compton, P. D., & Kelleher, N. L. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00698 · Cited by 88 · see citing works
Quantitative analysis of intact apolipoproteins in human HDL by top-down differential mass spectrometry
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
Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics
Melani, R. D., Skinner, O. S., Fornelli, L., Domont, G. B., Compton, P. D., & Kelleher, N. L. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.056523 · Cited by 85 · see citing works
The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics
LeDuc, R. D., Fellers, R. T., Early, B. P., Greer, J. B., Thomas, P. M., & Kelleher, N. L. (2014) · Journal of Proteome Research · doi:10.1021/pr401277r · Cited by 85 · see citing works
Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts
Ntai, I., LeDuc, R. D., Fellers, R. T., Erdmann-Gilmore, P., Davies, S. R., Rumsey, J. M., Early, B. P., Thomas, P. M., Li, S., Compton, P. D., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.047480 · Cited by 85 · see citing works
193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology
Morrison, L. J., & Brodbelt, J. S. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b03905 · Cited by 82 · see citing works
Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry
Cammarata, M. B., Thyer, R. T., Rosenberg, J. A., Ellington, A. D., & Brodbelt, J. S. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b04628 · Cited by 81 · 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-citation
Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins
Riley, N. M., Westphall, M. S., & Coon, J. J. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00881 · Cited by 80 · see citing works
Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation
Riley, N. M., Westphall, M. S., & Coon, J. J. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00249 · Cited by 79 · see citing works
Three Dimensional Liquid Chromatography Coupling Ion Exchange Chromatography/Hydrophobic Interaction Chromatography/Reverse Phase Chromatography for Effective Protein Separation in Top-Down Proteomics
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
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Tandem Mass Tag Protein Labeling for Top-Down Identification and Quantification
Hung, C., & Tholey, A. (2011) · Analytical Chemistry · doi:10.1021/ac202243r · Cited by 76 · see citing works
Top 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
Clinical Utility of Insulin-Like Growth Factor 1 and 2; Determination by High Resolution Mass Spectrometry
Bystrom, C. E., Sheng, S., Zhang, K., Caulfield, M. P., Clarke, N. J., & Reitz, R. E. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043457 · Cited by 76 · 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
Self-citation
Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression
Zheng, Y., Fornelli, L., Compton, P. D., Sharma, S., Canterbury, J., Mullen, C., Zabrouskov, V., Fellers, R. T., Thomas, P. M., Licht, J. D., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.053819 · Cited by 73 · see citing works
In-Line Separation by Capillary Electrophoresis Prior to Analysis by Top-Down Mass Spectrometry Enables Sensitive Characterization of Protein Complexes
Han, X., Wang, Y., Aslanian, A., Fonslow, B., Graczyk, B., Davis, T. N., & Yates, J. R. (2014) · Journal of Proteome Research · doi:10.1021/pr500971h · Cited by 72 · 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
Top-down venomics of the East African green mamba, Dendroaspis angusticeps , and the black mamba, Dendroaspis polylepis , highlight the complexity of their toxin arsenals
Petras, D., Heiss, P., Harrison, R. A., Süßmuth, R. D., & Calvete, J. J. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.06.018 · Cited by 71 · see citing works
Specific Enrichment of Phosphoproteins Using Functionalized Multivalent Nanoparticles
Hwang, L., Ayaz-Guner, S., Gregorich, Z. R., Cai, W., Valeja, S. G., Jin, S., & Ge, Y. (2015) · Journal of the American Chemical Society · doi:10.1021/ja511833y · Cited by 70 · see citing works
Self-citation
Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer
Fornelli, L., Ayoub, D., Aizikov, K., Liu, X., Damoc, E., Pevzner, P. A., Makarov, A., Beck, A., & Tsybin, Y. O. (2017) · Journal of Proteomics · doi:10.1016/j.jprot.2017.02.013 · Cited by 70 · see citing works
Evolving tRNASec for Efficient Canonical Incorporation of Selenocysteine
Thyer, R. T., Robotham, S. A., Brodbelt, J. S., & Ellington, A. D. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510695g · Cited by 69 · see citing works
Effective Protein Separation by Coupling Hydrophobic Interaction and Reverse Phase Chromatography for Top-down Proteomics
Xiu, 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-citation
Ligand binding to a G protein–coupled receptor captured in a mass spectrometer
Yen, H., Hopper, J. T. S., Liko, I., Allison, T. M., Zhu, Y., Wang, D., Stegmann, M., Mohammed, S., Wu, B., & Robinson, C. V. (2017) · Science Advances · doi:10.1126/sciadv.1701016 · Cited by 67 · see citing works
Front-End Electron Transfer Dissociation: A New Ionization Source
Earley, L., Anderson, L. C., Bai, D. L., Mullen, C., Syka, J. E. P., English, A. M., Dunyach, J., Stafford, G. C., Shabanowitz, J., Hunt, D. F., et al. (2013) · Analytical Chemistry · doi:10.1021/ac401783f · Cited by 67 · 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
Combine and Conquer: Surfactants, Solvents, and Chaotropes for Robust Mass Spectrometry Based Analyses of Membrane Proteins
Waas, M., Bhattacharya, S., Chuppa, S. L., Wu, X., Jensen, D. R., Omasits, U., Wollscheid, B., Volkman, B. F., Noon, K. R., & Gundry, R. L. (2014) · Analytical Chemistry · doi:10.1021/ac403185a · Cited by 66 · see citing works
Fast Top-Down Intact Protein Characterization with Capillary Zone Electrophoresis–Electrospray Ionization Tandem Mass Spectrometry
Sun, L., Knierman, M. D., Zhu, G., & Dovic̀hi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac4008122 · Cited by 65 · see citing works
An informatic framework for decoding protein complexes by top-down mass spectrometry
Skinner, O. S., Havugimana, P. C., Haverland, N. A., Fornelli, L., Early, B. P., Greer, J. B., Fellers, R. T., Durbin, K. R., do Vale, L. H. F., Melani, R. D., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3731 · Cited by 64 · see citing works
Resolubilization of Precipitated Intact Membrane Proteins with Cold Formic Acid for Analysis by Mass Spectrometry
Doucette, A. A., Vieira, D. B., Orton, D. J., & Wall, M. J. (2014) · Journal of Proteome Research · doi:10.1021/pr500864a · Cited by 63 · see citing works
High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics
Shen, Y., Tolić, N., Piehowski, P. D., Shukla, A. K., Kim, S., Zhao, R., Qu, Y., Robinson, E., Smith, R. D., & Paša-Tolić, L. (2017) · Journal of Chromatography A · doi:10.1016/j.chroma.2017.01.008 · Cited by 63 · see citing works
Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry
Haverland, N. A., Skinner, O. S., Fellers, R. T., Tariq, A., Early, B. P., LeDuc, R. D., Fornelli, L., Compton, P. D., & Kelleher, N. L. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1635-x · Cited by 63 · see citing works
Coupling Capillary Zone Electrophoresis to a Q Exactive HF Mass Spectrometer for Top-down Proteomics: 580 Proteoform Identifications from Yeast
Zhao, Y., Sun, L., Zhu, G., & Dovichi, N. J. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00493 · Cited by 61 · see citing works
Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments
Anderson, L. C., Karch, K. R., Ugrin, S. A., Coradin, M., English, A. M., Sidoli, S., Shabanowitz, J., Garcia, B. A., & Hunt, D. F. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o115.053843 · Cited by 60 · see citing works
Quantitative analysis of human salivary gland‐derived intact proteome using top‐down mass spectrometry
Wu, S., Brown, J. N., Tolić, N., Meng, D., Liu, X., Zhang, H., Zhao, R., Moore, R. J., Pevzner, P. A., Smith, R. D., et al. (2014) · PROTEOMICS · doi:10.1002/pmic.201300378 · Cited by 60 · see citing works
Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation
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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
Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements
Shortreed, M. R., Frey, B. L., Scalf, M., Knoener, R. A., Cesnik, A. J., & Smith, L. M. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b01090 · Cited by 58 · see citing works
Extraction, Enrichment, Solubilization, and Digestion Techniques for Membrane Proteomics
Moore, S., Hess, S., & Jorgenson, J. W. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b01122 · Cited by 57 · see citing works
Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry for Top-Down Characterization of the Mycobacterium marinum Secretome
Zhao, Y., Sun, L., Champion, M. M., Knierman, M. D., & Dovichi, N. J. (2014) · Analytical Chemistry · doi:10.1021/ac500092q · Cited by 56 · see citing works
Analysis of Monoclonal Antibodies in Human Serum as a Model for Clinical Monoclonal Gammopathy by Use of 21 Tesla FT-ICR Top-Down and Middle-Down MS/MS
He, L., Anderson, L. C., Barnidge, D. R., Murray, D. L., Hendrickson, C. L., & Marshall, A. G. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1602-6 · Cited by 56 · 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
Identification of Ultramodified Proteins Using Top-Down Tandem Mass Spectra
Liu, X., Hengel, S. M., Wu, S., Tolić, N., Paša‐Tolić, L., & Pevzner, P. A. (2013) · Journal of Proteome Research · doi:10.1021/pr400849y · Cited by 54 · see citing works
Protein characterization by on-line capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry.
Zhou, F., & Johnston, M. (2004) · Analytical Chemistry · doi:10.1021/ac035446n · Cited by 54 · see citing works
The Effect of Small Cations on the Positive Electrospray Responses of Proteins at Low pH
Pan, P., & McLuckey, S. A. (2003) · Analytical Chemistry · doi:10.1021/ac034344u · Cited by 53 · see citing works
Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics
Rhoads, T. W., Rose, C. M., Bailey, D. J., Riley, N. M., Molden, R. C., Nestler, A. J., Merrill, A. E., Smith, L. M., Hebert, A. S., Westphall, M. S., et al. (2014) · Analytical Chemistry · doi:10.1021/ac403579s · Cited by 52 · see citing works
Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation
Durbin, K. R., Skinner, O. S., Fellers, R. T., & Kelleher, N. L. (2015) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-015-1078-1 · Cited by 52 · see citing works
Top-Down Targeted Proteomics Reveals Decrease in Myosin Regulatory Light-Chain Phosphorylation That Contributes to Sarcopenic Muscle Dysfunction
Gregorich, Z. R., Peng, Y., Cai, W., Jin, Y., Wei, L., Chen, A. J., McKiernan, S. H., Aiken, J. M., Moss, R. L., Diffee, G. M., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00244 · Cited by 51 · see citing works
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Purification and High-Resolution Top-Down Mass Spectrometric Characterization of Human Salivary α-Amylase
Peng, Y., Chen, X., Sato, T., Rankin, S. A., Tsuji, R. F., & Ge, Y. (2012) · Analytical Chemistry · doi:10.1021/ac300083y · Cited by 51 · see citing works
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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
Submicrometer Particles and Slip Flow in Liquid Chromatography
Rogers, B. A., Wu, Z. J., Wei, B., et al. (2015) · Analytical Chemistry · doi:10.1021/ac504683d · Cited by 50 · see citing works
Native GELFrEE: A New Separation Technique for Biomolecular Assemblies
Skinner, O. S., do Vale, L. H. F., Catherman, A. D., Havugimana, P. C., de Sousa, M. V., Compton, P. D., & Kelleher, N. L. (2015) · Analytical Chemistry · doi:10.1021/ac504678d · Cited by 49 · see citing works
Native Top‐Down Mass Spectrometry of TAR RNA in Complexes with a Wild‐Type tat Peptide for Binding Site Mapping
Schneeberger, E., & Breuker, K. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201610836 · Cited by 47 · 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 & Cellular Proteomics · doi:10.1074/mcp.ra117.000124 · Cited by 47 · see citing works
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Controlled Ion Ejection from an External Trap for Extended m/z Range in FT-ICR Mass Spectrometry
Kaiser, N. K., Savory, J., & Hendrickson, C. L. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-014-0871-6 · Cited by 46 · see citing works
High-resolution separations of protein isoforms with liquid chromatography time-of-flight mass spectrometry using polymer monolithic capillary columns
Eeltink, S., Wouters, B., Desmet, G., Ursem, M., Blinco, D., Kemp, G. D., & Treumann, A. (2011) · Journal of Chromatography A · doi:10.1016/j.chroma.2011.06.049 · Cited by 45 · see citing works
Analysis of epididymal sperm maturation by MALDI profiling and top-down mass spectrometry
Labas, V., Spina, L., Belleannée, C., Teixeira‐Gomes, A., Gargaros, A., Dacheux, F., & Dacheux, J. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.09.031 · Cited by 44 · 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
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Integration of Ultraviolet Photodissociation with Proton Transfer Reactions and Ion Parking for Analysis of Intact Proteins
Holden, D. D., McGee, W. M., & Brodbelt, J. S. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03911 · Cited by 43 · see citing works
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra
Kou, Q., Wu, S., Tolić, N., Paša‐Tolić, L., Liu, Y., & Liu, X. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw806 · Cited by 43 · see citing works
Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients
Toby, T. K., Abecassis, M., Kim, K., Thomas, P. M., Fellers, R. T., LeDuc, R. D., Kelleher, N. L., Demetris, J., & Levitsky, J. (2017) · American Journal of Transplantation · doi:10.1111/ajt.14359 · 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
Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS
Dang, X., Singh, A., Spetman, B. D., Nolan, K. D., Isaacs, J. S., Dennis, J. H., Dalton, S., Marshall, A. G., & Young, N. L. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00414 · Cited by 41 · see citing works
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Authors: Chen, B., Brown, K. A., Lin, Z., & Ge, Y.
Affiliations: University of Wisconsin–Madison (US)
Corresponding author: Ge, Ying
ORCID: Chen, Bifan
Brown, Kyle A.
Lin, Ziqing
Ge, Ying
Venue: Analytical Chemistry
Publisher: American Chemical Society (ACS)
Published: 2017-11-21
Volume: 90
Issue: 1
Pages: 110-127
ISSN: 0003-2700 (ISSN-L)
1520-6882
DOI: 10.1021/acs.analchem.7b04747
PMC: PMC6138622
OpenAlex: W2769766412
Cited by: 210
References: 190
Citations by year: 2026: 18 · 2025: 17 · 2024: 16 · 2023: 25 · 2022: 26 · 2021: 34 · 2020: 29 · 2019: 25 · 2018: 18 · 2015: 1 · 2012: 1
FWCI: 2.29
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: Analytical Chemistry (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of Health (R01GM117058, R0HL096971, R01HL109810, S10OD018475)
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 › Advanced Biosensing Techniques and Applications
Keywords: top-down proteomics, protein structure analysis, mass spectrometry
MeSH terms: Humans, Proteomics

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Top-Down Proteomics: Ready for Prime Time?

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