Production of Over 27 000 Peptide and Nearly 4400 Protein Identifications by Single-Shot Capillary-Zone Electrophoresis–Mass Spectrometry via Combination of a Very-Low-Electroosmosis Coated Capillary, a Third-Generation Electrokinetically-Pumped Sheath-Flow Nanospray Interface, an Orbitrap Fusion Lumos Tribrid Mass Spectrometer, and an Advanced-Peak-Determination Algorithm

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484 · 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

MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., & Mechtler, K. (2014) · Journal of Proteome Research · doi:10.1021/pr500202e · Cited by 477 · see citing works

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., & Aebersold, R. (2009) · Nature · doi:10.1038/nature08184 · Cited by 421 · 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

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

Single‐Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16‐Cell Frog (<i>Xenopus</i>) Embryo

Lombard‐Banek, C., Moody, S. A., & Nemes, P. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201510411 · Cited by 214 · see citing works

Velocity-Difference Induced Focusing of Nucleotides in Capillary Electrophoresis with a Dynamic pH Junction

Britz‐McKibbin, P., Bebault, G. M., & Chen, D. D. Y. (2000) · Analytical Chemistry · doi:10.1021/ac991104z · Cited by 201 · see citing works

Improving the Comprehensiveness and Sensitivity of Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry for Proteomic Analysis

Wang, Y., Fonslow, B. R., Wong, C. C. L., Nakorchevsky, A., & Yates, J. R. (2012) · Analytical Chemistry · doi:10.1021/ac301091m · Cited by 144 · see citing works

Now, More Than Ever, Proteomics Needs Better Chromatography

Shishkova, E., Hebert, A. S., & Coon, J. J. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.007 · Cited by 140 · see citing works

Trends in ultrasensitive proteomics

Altelaar, M. A. F., & Heck, A. J. R. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.12.011 · Cited by 139 · see citing works

The Revolution and Evolution of Shotgun Proteomics for Large-Scale Proteome Analysis

Yates, J. R. (2013) · Journal of the American Chemical Society · doi:10.1021/ja3094313 · Cited by 131 · see citing works

Single-Shot Proteomics Using Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry with Production of More than 1 250 <i>Escherichia coli</i> Peptide Identifications in a 50 min Separation

Zhu, G., Sun, L., Yan, X., & Dovichi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac303750g · Cited by 103 · see citing works

Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

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

Bottom-Up Proteomics of <i>Escherichia coli</i> 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

Detachable Strong Cation Exchange Monolith, Integrated with Capillary Zone Electrophoresis and Coupled with pH Gradient Elution, Produces Improved Sensitivity and Numbers of Peptide Identifications during Bottom-up Analysis of Complex Proteomes

Zhang, Z., Yan, X., Sun, L., Zhu, G., & Dovichi, N. J. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00789 · Cited by 67 · see citing works

Improved Precursor Characterization for Data-Dependent Mass Spectrometry

Hebert, A. S., Thöing, C., Riley, N. M., Kwiecien, N. W., Shiskova, E., Huguet, R., Cardasis, H. L., Kuehn, A., Eliuk, S., Zabrouskov, V., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04808 · Cited by 67 · see citing works

Integrated strong cation-exchange hybrid monolith coupled with capillary zone electrophoresis and simultaneous dynamic pH junction for large-volume proteomic analysis by mass spectrometry

Zhang, Z., Sun, L., Zhu, G., Yan, X., & Dovichi, N. J. (2015) · Talanta · doi:10.1016/j.talanta.2015.01.040 · Cited by 53 · see citing works

Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis

Krokhin, O. V., Anderson, G., Spicer, V., Sun, L., & Dovichi, N. J. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.6b04544 · Cited by 53 · see citing works

Strong cation exchange-reversed phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry platform with high peak capacity for deep bottom-up proteomics

Chen, D., Shen, X., & Sun, L. (2018) · Analytica Chimica Acta · doi:10.1016/j.aca.2018.01.037 · Cited by 47 · see citing works

Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis

Zhang, Z., Sun, L., Zhu, G., Cox, O. F., Huber, P. W., & Dovic̀hi, N. J. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03496 · Cited by 46 · 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

Surface-Confined Aqueous Reversible Addition–Fragmentation Chain Transfer (SCARAFT) Polymerization Method for Preparation of Coated Capillary Leads to over 10 000 Peptides Identified from 25 ng HeLa Digest by Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry

Zhang, Z., Peuchen, E. H., & Dovic̀hi, N. J. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b01147 · Cited by 29 · see citing works

Multisegment injections improve peptide identification rates in capillary zone electrophoresis-based bottom-up proteomics

Boley, D. A., Zhang, Z., & Dovichi, N. J. (2017) · Journal of Chromatography A · doi:10.1016/j.chroma.2017.07.022 · Cited by 29 · see citing works

Enhancing Proteomic Throughput in Capillary Electrophoresis–Mass Spectrometry by Sequential Sample Injection

Faserl, K., Sarg, B., Solá, L., & Lindner, H. H. (2017) · PROTEOMICS · doi:10.1002/pmic.201700310 · Cited by 29 · see citing works

Optimization of mass spectrometric parameters improve the identification performance of capillary zone electrophoresis for single-shot bottom-up proteomics analysis

Zhang, Z., & Dovichi, N. J. (2018) · Analytica Chimica Acta · doi:10.1016/j.aca.2017.11.023 · Cited by 20 · see citing works

Single-cell Proteomics: Progress and Prospects

Kelly, R. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r120.002234 · Cited by 360 · see citing works

Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research

Gomes, F. P., & Yates, J. R. (2019) · Mass Spectrometry Reviews · doi:10.1002/mas.21599 · Cited by 112 · see citing works

Challenging Bioanalyses with Capillary Electrophoresis

Kristoff, C. J., Bwanali, L., Veltri, L. M., Gautam, G. P., Rutto, P. K., Newton, E. O., & Holland, L. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b04718 · Cited by 75 · see citing works

Improved Sensitivity of Ultralow Flow LC–MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology

Greguš, M., Kostas, J. C., Ray, S., Abbatiello, S. E., & Ivanov, A. R. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c03262 · Cited by 71 · see citing works

Capillary zone electrophoresis-mass spectrometry for bottom-up proteomics

Zhang, Z., Qu, Y., & Dovichi, N. J. (2018) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2018.08.008 · Cited by 61 · see citing works

Recent Advances and New Perspectives in Capillary Electrophoresis-Mass Spectrometry for Single Cell “Omics”

DeLaney, K., Sauer, C. S., Vu, N. Q., & Li, L. (2018) · Molecules · doi:10.3390/molecules24010042 · Cited by 56 · see citing works

Miniaturized Filter-Aided Sample Preparation (MICRO-FASP) Method for High Throughput, Ultrasensitive Proteomics Sample Preparation Reveals Proteome Asymmetry in Xenopus laevis Embryos

Zhang, Z., Dubiak, K. M., Huber, P. W., & Dovic̀hi, N. J. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00470 · Cited by 52 · see citing works

Recent developments in capillary and microchip electroseparations of peptides (2017–mid 2019)

Kašička, V. (2019) · Electrophoresis · doi:10.1002/elps.201900269 · Cited by 49 · see citing works

Advances in capillary electrophoresis-mass spectrometry for cell analysis

Zhou, W., Zhang, B., Liu, Y., Wang, C., Sun, W., Li, W., & Chen, Z. (2019) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2019.05.011 · Cited by 45 · see citing works

Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid‐2018–2022)

Štěpánová, S., & Kašička, V. (2023) · Journal of Separation Science · doi:10.1002/jssc.202300043 · Cited by 40 · see citing works

Capillary Zone Electrophoresis–Tandem Mass Spectrometry for Large-Scale Phosphoproteomics with the Production of over 11,000 Phosphopeptides from the Colon Carcinoma HCT116 Cell Line

Chen, D., Ludwig, K. R., Krokhin, O. V., Spicer, V., Yang, Z., Shen, X., Hummon, A. B., & Sun, L. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.8b04770 · Cited by 34 · see citing works

Peptide mapping of proteins by capillary electromigration methods

Kašička, V. (2022) · Journal of Separation Science · doi:10.1002/jssc.202200664 · Cited by 32 · see citing works

Data-Dependent Acquisition Ladder for Capillary Electrophoresis Mass Spectrometry-Based Ultrasensitive (Neuro)Proteomics

Choi, S. B., Muñoz-LLancao, P., Manzini, M. C., & Nemes, P. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c03327 · Cited by 31 · see citing works

Improved Nanoflow RPLC-CZE-MS/MS System with High Peak Capacity and Sensitivity for Nanogram Bottom-up Proteomics

Yang, Z., Shen, X., Chen, D., & Sun, L. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00545 · Cited by 27 · see citing works

Single-Shot Capillary Zone Electrophoresis–Tandem Mass Spectrometry Produces over 4400 Phosphopeptide Identifications from a 220 ng Sample

Zhang, Z., Hebert, A. S., Westphall, M. S., Coon, J. J., & Dovichi, N. J. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00244 · Cited by 22 · see citing works

Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data‐dependent proteomics

Huang, P., Liu, C., Gao, W., Chu, B., Cai, Z., & Tian, R. (2020) · Journal of Mass Spectrometry · doi:10.1002/jms.4653 · Cited by 17 · see citing works

Bottom‐up proteomics of envelope proteins extracted from spinach chloroplast via high organic content CE‐MS

Cheng, J., Morin, G. B., & Chen, D. D. Y. (2020) · Electrophoresis · doi:10.1002/elps.201900452 · Cited by 15 · see citing works

Fully automated sample treatment method for high throughput proteome analysis

Yuan, H., Dai, Z., Zhang, X., Zhao, B., Chu, H., Zhang, L., & Zhang, Y. (2020) · Science China Chemistry · doi:10.1007/s11426-020-9878-8 · Cited by 10 · see citing works

Seamlessly Integrated Miniaturized Filter-Aided Sample Preparation Method to Fractionation Techniques for Fast, Loss-Less, and In-Depth Proteomics Analysis of 1 μg of Cell Lysates at Low Cost

Zhang, Z., & Dovic̀hi, N. J. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c01396 · Cited by 8 · see citing works

SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides

Serrano, L. R., Mellors, J. S., Thompson, J. W., Lancaster, N. M., Robinson, M. L., Overmyer, K. A., Quarmby, S. T., & Coon, J. J. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00194 · Cited by 8 · see citing works

Online protein digestion in membranes between capillary electrophoresis and mass spectrometry

Ryan, K. A., & Bruening, M. L. (2023) · The Analyst · doi:10.1039/d3an00106g · Cited by 6 · see citing works

Standard Flow Multiplexed Proteomics (SFloMPro)—An Accessible Alternative to NanoFlow Based Shotgun Proteomics

Orsburn, B. C., Miller, S. D., & Jenkins, C. (2022) · Proteomes · doi:10.3390/proteomes10010003 · Cited by 6 · see citing works

Capillary zone electrophoresis-tandem mass spectrometry for in-depth proteomics analysis via data-independent acquisition

Liu, R., Lü, G., Hu, X., Li, J., Zhang, Z., & Tang, K. (2024) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-024-05502-7 · Cited by 4 · see citing works

Preparation and Evaluation of 2 m Long Open Tubular Capillary Columns of 50 μm Internal Diameter for Separation of Peptides in Liquid Chromatography

Ali, A., Sun, G., Kim, J. S., Kim, Y. S., An, H. J., & Cheong, W. J. (2021) · Chromatographia · doi:10.1007/s10337-020-04003-w · Cited by 3 · see citing works

Capillary Electrophoresis-Mass Spectrometry for Cancer Metabolomics

Xu, X. (2021) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-51652-9_13 · Cited by 3 · see citing works

Integrated MICROFASP Method with CZE-Based Fractionation Technique and NanoRPLC-ESI-MS/MS for a Comprehensive Proteomics Analysis of a Submicrogram Sample

Lü, G., Ying, G., He, Y., Li, Y., & Zhang, Z. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00396 · Cited by 2 · see citing works

Technique Development of High-Throughput and High-Sensitivity Sample Preparation and Separation for Proteomics

Zhang, Z., Zheng, M., Zhao, Y., & Wang, P. G. (2021) · Bioanalysis · doi:10.4155/bio-2021-0202 · Cited by 1 · see citing works

A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)ProteomicsPreprint

Choi, S. B., Muñoz-LLancao, P., Manzini, M. C., & Nemes, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.03.454943 · Cited by 1 · see citing works

SPE-CZE-MS quantifies zeptomole concentrations of phosphorylated peptidesPreprint

Serrano, L. R., Mellors, J. S., Thompson, J. W., Lancaster, N. M., Robinson, M. L., Overmyer, K. A., Quarmby, S. T., & Coon, J. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.07.627347 · Cited by 1 · see citing works

Development of high-sensitivity CE-ESI-MS-based methods for proteomic profiling of limited samples and single cells

Johnson, K. R. (2022) · doi:10.17760/d20467259

Single-Shot Proteomics Using Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry with Production of More than 1 250 <i>Escherichia coli</i> Peptide Identifications in a 50 min Separation

Zhu, G., Sun, L., Yan, X., & Dovichi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac303750g · Cited by 103 · see citing works

Protein Identification by Capillary Zone Electrophoresis/Microelectrospray Ionization-Tandem Mass Spectrometry at the Subfemtomole Level

Figeys, D., van Oostveen, I., Ducret, A., & Aebersold, R. H. (1996) · Analytical Chemistry · doi:10.1021/ac960191h · Cited by 135 · see citing works

Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

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 · doi:10.1002/ange.201409075 · Cited by 11 · see citing works

Protein and Peptide Identification by Capillary Zone Electrophoresis-Tandem Mass Spectrometry.

Liu, T., Zeng, R., Shao, X., & Xia, Q. (1999) · PubMed · Cited by 1 · see citing works

Stable, reproducible, and automated capillary zone electrophoresis–tandem mass spectrometry system with an electrokinetically pumped sheath–flow nanospray interface

Zhu, G., Sun, L., Yan, X., & Dovic̀hi, N. J. (2013) · Analytica Chimica Acta · doi:10.1016/j.aca.2013.11.057 · Cited by 20 · see citing works