Coupling Capillary Zone Electrophoresis to a Q Exactive HF Mass Spectrometer for Top-down Proteomics: 580 Proteoform Identifications from Yeast

Zhao, Yimeng; Sun, Liangliang; Zhu, Guijie; Dovichi, Norman J.

doi:10.1021/acs.jproteome.6b00493

Cited by 61Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMicrofluidic and Capillary Electrophoresis Applications

Coupling Capillary Zone Electrophoresis to a Q Exactive HF Mass Spectrometer for Top-down Proteomics: 580 Proteoform Identifications from Yeast

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Zhao, Yimeng, Sun, Liangliang, Zhu, Guijie, Dovichi, Norman J.·2016·Journal of Proteome Research

DOI 10.1021/acs.jproteome.6b00493PMC PMC5075424

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Abstract

We used reversed-phase liquid chromatography to separate the yeast proteome into 23 fractions. These fractions were then analyzed using capillary zone electrophoresis (CZE) coupled to a Q-Exactive HF mass spectrometer using an electrokinetically pumped sheath flow interface. The parameters of the mass spectrometer were first optimized for top-down proteomics using a mixture of seven model proteins; we observed that intact protein mode with a trapping pressure of 0.2 and normalized collision energy of 20% produced the highest intact protein signals and most protein identifications. Then, we applied the optimized parameters for analysis of the fractionated yeast proteome. From this, 580 proteoforms and 180 protein groups were identified via database searching of the MS/MS spectra. This number of proteoform identifications is two times larger than that of previous CZE-MS/MS studies. An additional 3,243 protein species were detected based on the parent ion spectra. Post-translational modifications including N-terminal acetylation, signal peptide removal, and oxidation were identified.

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Jorgenson, J. W., & Lukacs, K. D. (1983) · Science · doi:10.1126/science.6623076 · Cited by 1,289 · 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
Top Down versus Bottom Up Protein Characterization by Tandem High-Resolution Mass Spectrometry
Kelleher, N. L., Lin, H., Valaskovic, G. A., Aaserud, D. J., Fridriksson, E. K., & McLafferty, F. W. (1999) · Journal of the American Chemical Society · doi:10.1021/ja973655h · Cited by 606 · 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
System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap
Nagaraj, N., Alexander Kulak, N., Cox, J., Neuhauser, N., Mayr, K., Hoerning, O., Vorm, O., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013722 · Cited by 392 · see citing works
Peer Reviewed: Top-Down Proteomics
Kelleher, N. (2004) · Analytical Chemistry · doi:10.1021/ac0415657 · Cited by 386 · see citing works
Top Down Characterization of Larger Proteins (45 kDa) by Electron Capture Dissociation Mass Spectrometry
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
Extending 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
Top Down Proteomics
Yates, J. R., & Kelleher, N. L. (2013) · Analytical Chemistry · doi:10.1021/ac401484r · Cited by 324 · see citing works
Simplifying CE−MS Operation. 2. Interfacing Low-Flow Separation Techniques to Mass Spectrometry Using a Porous Tip
Moini, M. (2007) · Analytical Chemistry · doi:10.1021/ac0704560 · Cited by 322 · see citing works
Tuberculous Granuloma Formation Is Enhanced by a Mycobacterium Virulence Determinant
Volkman, H. E., Clay, H., Beery, D., Chang, J. C., Sherman, D. R., & Ramakrishnan, L. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020367 · Cited by 311 · see citing works
Selective Focusing of Catecholamines and Weakly Acidic Compounds by Capillary Electrophoresis Using a Dynamic pH Junction
Britz‐McKibbin, P., & Chen, D. D. Y. (2000) · Analytical Chemistry · doi:10.1021/ac990898e · Cited by 310 · see citing works
Simplified capillary electrophoresis nanospray sheath‐flow interface for high efficiency and sensitive peptide analysis
Wojcik, R., Dada, O. O., Sadilek, M., & Dovichi, N. J. (2010) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.4672 · Cited by 234 · see citing works
Self-citation
Third-Generation Electrokinetically Pumped Sheath-Flow Nanospray Interface with Improved Stability and Sensitivity for Automated Capillary Zone Electrophoresis–Mass Spectrometry Analysis of Complex Proteome Digests
Sun, L., Zhu, G., Zhang, Z., Mou, S., & Dovichi, N. J. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00100 · Cited by 216 · see citing works
Self-citation
Ultrasensitive and Fast Bottom‐up Analysis of Femtogram Amounts of Complex Proteome Digests
Sun, L., Zhu, G., Zhao, Y., Yan, X., Mou, S., & Dovichi, N. J. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201308139 · Cited by 212 · see citing works
Self-citation
Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation
Tran, J. C., & Doucette, A. A. (2008) · Analytical Chemistry · doi:10.1021/ac702197w · Cited by 206 · see citing works
Analysis of dilute peptide samples by capillary zone electrophoresis
Aebersold, R., & Morrison, H. D. (1990) · Journal of Chromatography A · doi:10.1016/s0021-9673(01)90206-7 · Cited by 179 · 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
Capillary electrophoresis and isoelectric focusing in peptide and protein analysis
Righetti, P. G., Sebastiano, R., & Citterio, A. (2012) · PROTEOMICS · doi:10.1002/pmic.201200378 · Cited by 166 · see citing works
Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions
Ansong, 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
Protein 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
Low-Flow Sheathless Capillary Electrophoresis–Mass Spectrometry for Sensitive Glycoform Profiling of Intact Pharmaceutical Proteins
Haselberg, R., de Jong, G. J., & Somsen, G. W. (2013) · Analytical Chemistry · doi:10.1021/ac303158f · Cited by 149 · see citing works
Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry as an Alternative Proteomics Platform to Ultraperformance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry for Samples of Intermediate Complexity
Li, Y., Champion, M. M., Sun, L., Champion, P. A. D., Wojcik, R., & Dovichi, N. J. (2012) · Analytical Chemistry · doi:10.1021/ac202899p · Cited by 128 · see citing works
Self-citation
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Zhu, G., Sun, L., Yan, X., & Dovichi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac303750g · Cited by 103 · see citing works
Self-citation
Interaction of capillary zone electrophoresis with a sheath flow cuvette detector
Cheng, Y. F., Wu, S., Chen, D. D. Y., & Dovic̀hi, N. J. (1990) · Analytical Chemistry · doi:10.1021/ac00204a014 · Cited by 98 · see citing works
Self-citation
Optimizing capillary electrophoresis for top‐down proteomics of 30–80 kDa proteins
Li, Y., Compton, P. D., Tran, J. C., Ntai, I., & Kelleher, N. L. (2014) · PROTEOMICS · doi:10.1002/pmic.201300381 · Cited by 95 · see citing works
Thermally-initiated free radical polymerization for reproducible production of stable linear polyacrylamide coated capillaries, and their application to proteomic analysis using capillary zone electrophoresis–mass spectrometry
Zhu, G., Sun, L., & Dovic̀hi, N. J. (2015) · Talanta · doi:10.1016/j.talanta.2015.06.003 · Cited by 91 · see citing works
Self-citation
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Sun, L., Hebert, A. S., Yan, X., Zhao, Y., Westphall, M. S., Rush, M. J. P., Zhu, G., Champion, M. M., Coon, J. J., & Dovic̀hi, N. J. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201409075 · Cited by 91 · see citing works
Self-citation
Bottom-Up Proteomics of Escherichia coli Using Dynamic pH Junction Preconcentration and Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry
Zhu, G., Sun, L., Yan, X., & Dovichi, N. J. (2014) · Analytical Chemistry · doi:10.1021/ac5004486 · Cited by 78 · see citing works
Self-citation
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Han, X., Wang, Y., Aslanian, A., Bern, M., Lavallée-Adam, M., & Yates, J. R. (2014) · Analytical Chemistry · doi:10.1021/ac503439n · Cited by 77 · 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
Analyzing Protein Micro-Heterogeneity in Chicken Ovalbumin by High-Resolution Native Mass Spectrometry Exposes Qualitatively and Semi-Quantitatively 59 Proteoforms
Yang, Y., Barendregt, A., Kamerling, J. P., & Heck, A. J. R. (2013) · Analytical Chemistry · doi:10.1021/ac403057y · Cited by 68 · 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
Self-citation
Robust Analysis of the Yeast Proteome under 50 kDa by Molecular-Mass-Based Fractionation and Top-Down Mass Spectrometry
Kellie, J. F., Catherman, A. D., Durbin, K. R., Tran, J. C., Tipton, J., Norris, J. L., Witkowski, C. E., Thomas, P. M., & Kelleher, N. (2011) · Analytical Chemistry · doi:10.1021/ac202384v · Cited by 62 · 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
Self-citation
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
Self-citation
Fast separation and analysis of reduced monoclonal antibodies with capillary zone electrophoresis coupled to mass spectrometry
Zhao, Y., Sun, L., Knierman, M. D., & Dovichi, N. J. (2016) · Talanta · doi:10.1016/j.talanta.2015.11.020 · Cited by 49 · see citing works
Self-citation
Characterization of proteins from Spirulina platensis microalga using capillary electrophoresis‐ion trap‐mass spectrometry and capillary electrophoresis‐time of flight‐mass spectrometry
Simó, C., Herrero, M., Neusüß, C., Pelzing, M., Kenndler, E., Barbas, C., Ibáñez, E., & Cifuentes, A. (2005) · Electrophoresis · doi:10.1002/elps.200500055 · Cited by 45 · see citing works
Bottom‐up proteome analysis of E . coli using capillary zone electrophoresis‐tandem mass spectrometry with an electrokinetic sheath‐flow electrospray interface
Yan, X., Essaka, D. C., Sun, L., Zhu, G., & Dovic̀hi, N. J. (2013) · PROTEOMICS · doi:10.1002/pmic.201300062 · Cited by 40 · see citing works
Self-citation
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line
Sun, L., Zhu, G., Mou, S., Zhao, Y., Champion, M. M., & Dovic̀hi, N. J. (2014) · Journal of Chromatography A · doi:10.1016/j.chroma.2014.07.024 · Cited by 31 · see citing works
Self-citation
Coupling immobilized alkaline phosphatase-based automated diagonal capillary electrophoresis to tandem mass spectrometry for phosphopeptide analysis
Mou, S., Sun, L., Wojcik, R., & Dovic̀hi, N. J. (2013) · Talanta · doi:10.1016/j.talanta.2013.08.001 · Cited by 22 · see citing works
Self-citation
Capillary Zone Electrophoresis as A Tool for Bottom-Up Protein Analysis
Wojcik, R., Zhu, G., Zhang, Z., Yan, X., Zhao, Y., Sun, L., Champion, M. M., & Dovic̀hi, N. J. (2015) · Bioanalysis · doi:10.4155/bio.15.227 · Cited by 16 · see citing works
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Brodbelt, J. S. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04563 · Cited by 245 · 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
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Chen, B., Brown, K. A., Lin, Z., & Ge, Y. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04747 · Cited by 210 · see citing works
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Breadmore, M. C., Grochocki, W., Kalsoom, U., Alves, M. N., Phung, S. C., Tehranirokh, M., Cabot, J. M., Ghiasvand, A., Li, F., Shallan, A. I., et al. (2018) · Electrophoresis · doi:10.1002/elps.201800384 · Cited by 136 · see citing works
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Dawod, M., Arvin, N. E., & Kennedy, R. T. (2017) · The Analyst · doi:10.1039/c7an00198c · Cited by 132 · see citing works
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Martelli, C., & Desiderio, C. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809375-7.00014-9 · Cited by 5 · see citing works
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Faculty Opinions recommendation of High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer.
Yates, J. R. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727514046.793557932
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Ruel, C. (2018) · doi:10.70675/bbbf66daz24dfz4f61z8146z3e537087ba11

Authors: Zhao, Y., Sun, L., Zhu, G., & Dovichi, N. J.
Affiliations: University of Notre Dame (US)
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
ORCID: Zhao, Yimeng
Sun, Liangliang
Venue: Journal of Proteome Research
Publisher: American Chemical Society (ACS)
Published: 2016-08-25
Volume: 15
Issue: 10
Pages: 3679-3685
ISSN: 1535-3893 (ISSN-L)
1535-3907
DOI: 10.1021/acs.jproteome.6b00493
PMC: PMC5075424
OpenAlex: W2488918761
Semantic Scholar: 03aac7c7cb4ba9850e6d7ba35ba6a7c6211346af
Cited by: 61
References: 42
Citations by year: 2026: 2 · 2025: 4 · 2024: 3 · 2023: 3 · 2022: 4 · 2021: 2 · 2020: 3 · 2019: 13 · 2018: 13 · 2017: 11 · 2016: 2 · 2015: 1
FWCI: 6.47
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Journal of Proteome Research (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of General Medical Sciences (R01GM096767)
Topics: Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Physical Sciences › Engineering › Biomedical Engineering › Microfluidic and Capillary Electrophoresis Applications
Keywords: top-down proteomics, capillary zone electrophoresis, yeast proteome, proteoform identification, protein fractionation, reversed-phase liquid chromatography, post-translational modification, N-terminal acetylation, signal peptide removal, protein oxidation
MeSH terms: Fungal Proteins, Protein Processing, Post-Translational, Saccharomyces cerevisiae, Electrophoresis, Capillary, Proteome, Proteomics, Tandem Mass Spectrometry

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Coupling Capillary Zone Electrophoresis to a Q Exactive HF Mass Spectrometer for Top-down Proteomics: 580 Proteoform Identifications from Yeast

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