• This record comes from PubMed

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

. 2023 Jun ; 46 (12) : e2300043. [epub] 20230304

Language English Country Germany Media print-electronic

Document type Review, Journal Article

Grant support
20-03899S Czech Science Foundation
RVO 61388963 Czech Academy of Sciences

This review gives a wide overview of recent advances and applications of capillary electrophoresis and microchip capillary electrophoresis methods in the fields of proteomics and peptidomics in the period from mid-2018 up to the end of 2022. The methodological topics covering sample preparation and concentration techniques, hyphenation of capillary electrophoresis methods with mass spectrometry, and multidimensional separations by on-line or off-line coupled different capillary electrophoresis and liquid chromatography techniques are described and new developments in both bottom-up and top-down approaches in proteomics are presented. In addition, various applications of capillary electrophoresis methods in proteomic and peptidomic studies are demonstrated. They include monitoring of protein posttranslational modifications and applications in biological and biochemical research, clinical peptidomics and proteomics, and food analysis.

See more in PubMed

Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotech. 1999;17:121-7.

Bradshaw RA, Burlingame AL. From proteins to proteomics. IUBMB Life. 2005;57:267-72.

Zhang YY, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev. 2013;113:2343-94.

Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH. Proteomics: technologies and their applications. J Chromatogr Sci. 2017;55:182-96.

Drown BS, Jooss K, Melani RD, Lloyd-Jones C, Camarillo JM, Kelleher NL. Mapping the proteoform landscape of five human tissues. J Proteome Res. 2022;21:1299-310.

Schrader M, Fricker L, editors. Peptidomics: methods and strategies. New York: Humana Press Inc.; 2018.

Schrader M. Origins, technological development, and applications of peptidomics, in: Schrader M, Fricker L, editors. Peptidomics: methods and strategies, New York: Humana Press Inc.; 2018. pp. 3-39.

Fricker L. Quantitative peptidomics: General considerations, in: Schrader M, Fricker L, editors. Peptidomics: methods and strategies. New York: Humana Press Inc.; 2018. pp. 121-40.

Vitorino R, Choudhury M, Guedes S, Ferreira R, Thongboonkerd V, Sharma L, et al. Peptidomics and proteogenomics: background, challenges and future needs. Expert Rev Proteomics 2021;18:643-59.

Dams M, Dores-Sousa JL, Lamers RJ, Treumann A, Eeltink S. High-resolution nano-liquid chromatography with tandem mass spectrometric detection for the bottom-up analysis of complex proteomic samples. Chromatographia 2019;82:101-10.

Xiang PL, Zhu Y, Yang Y, Zhao ZT, Williams SM, Moore RJ, et al. Picoflow liquid chromatography-mass spectrometry for ultrasensitive bottom-up proteomics using 2-mu m-i.d. open tubular columns. Anal Chem. 2020;92:4711-5.

Nice EC. The separation sciences, the front end to proteomics: an historical perspective. Biomed Chromatogr. 2020;35:e4995.

Lenco J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholous P, et al. Reversed-phase liquid chromatography of peptides for bottom-up proteomics: a tutorial. J Proteome Res. 2022;21:2846-92.

Chen DY, Mccool EN, Yang ZC, Shen XJ, Lubeckyj RA, Xu T, et al. Recent advances (2019-2021) of capillary electrophoresis-mass spectrometry for multilevel proteomics. Mass Spectrom Rev. 2023;42:617-42. https://doi.org/10.1002/mas.21714

Xu T, Sun LL. A mini review on capillary isoelectric focusing-mass spectrometry for top-down proteomics. Front Che. 2021;9:651757.

Stepanova S, Kasicka V. Peptidomics and capillary electrophoresis, in: Simionato AVC, editor. Separation techniques applied to omics sciences: from principles to relevant applications. Cham: Springer International Publishing Ag. 2021. pp. 87-104.

Chen H, Shi PJ, Fan FJ, Tu ML, Xu Z, Xu XB, et al. Complementation of Uplc-Q-Tof-Ms and Cesi-Q-Tof-Ms on identification and determination of peptides from Bovine Lactoferrin. J Chromatogr B. 2018;1084:150-7.

Miksik I. Coupling of CE-MS for protein and peptide analysis. J Sep Sci. 2019;42:385-97.

Kasicka V. Recent developments in capillary and microchip electroseparations of peptides (2019-mid 2021). Electrophoresis 2022;43:82-108.

Stepanova S, Kasicka V. Applications of capillary electromigration methods for separation and analysis of proteins (2017-mid 2021) - a review. Anal Chim Acta. 2022;1209:339447.

Kasicka V. Recent developments in capillary and microchip electroseparations of peptides (2017-mid 2019). Electrophoresis 2020;41:10-35.

Stolz A, Jooss K, Hocker O, Romer J, Schlecht J, Neususs C. Recent advances in capillary electrophoresis-mass spectrometry: instrumentation, methodology and applications. Electrophoresis 2019;40:79-112.

Kristoff CJ, Bwanali L, Veltri LM, Gautam GP, Rutto PK, Newton EO, et al. Challenging bioanalyses with capillary electrophoresis Anal Chem. 2020;92:49-66.

Johnson KR, Gregus M, Kostas JC, Ivanov AR. Capillary electrophoresis coupled to electrospray ionization tandem mass spectrometry for ultra-sensitive proteomic analysis of limited samples. Anal Chem. 2022;94:704-13.

Lubeckyj RA, Basharat AR, Shen XJ, Liu XW, Sun LL. Large-scale qualitative and quantitative top-down proteomics using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry with nanograms of proteome samples. J Am Soc Mass Spectrom. 2019;30:1435-45.

Kartsova LA, Makeeva DV, Bessonova EA. Current status of capillary electrophoresis J Anal Chem. 2020;75:1497-513.

Wang MY, Gong Q, Liu WF, Tan SW, Xiao J, Chen CP. Applications of capillary electrophoresis in the fields of environmental, pharmaceutical, clinical, and food analysis (2019-2021). J Sep Sci. 2022;45:1918-41.

Gao ZT, Zhong WW. Recent (2018-2020) development in capillary electrophoresis. Anal Bioanal Chem. 2022;414:115-30.

Specht H, Slavov N. Transformative opportunities for single-cell proteomics. J Proteome Res. 2018;17:2565-71.

DeLaney K, Sauer CS, Vu NQ, Li LJ. Recent advances and new perspectives in capillary electrophoresis-mass spectrometry for single cell “omics”. Molecules 2019;24:42.

Lombard-Banek C, Choi SB, Nemes P. in: Allbritton NL, Kovarik ML, editors. Enzyme activity in single cells. Cambridge, MA: Academic Press; 2019. pp. 263-92.

Shen BW, Pade LR, Choi SB, Munoz-LLancao P, Manzini MC, Nemes P. Capillary electrophoresis mass spectrometry for scalable single-cell proteomics. Front Chem. 2022;10:863979.

Cupp-Sutton KA, Fang ML, Wu S. Separation methods in single-cell proteomics: RPLC or CE? Int J Mass Spectrom. 2022;481:116920.

Amenson-Lamar EA, Sun LL, Zhang Z, Bohn PW, Dovichi NJ. Detection of 1 zmol injection of angiotensin using capillary zone electrophoresis coupled to a Q-Exactive HF mass spectrometer with an electrokinetically pumped sheath-flow electrospray interface. Talanta 2019;204:70-3.

Choi SB, Munoz-LLancao P, Manzini MC, Nemes P. Data-dependent acquisition ladder for capillary electrophoresis mass spectrometry-based ultrasensitive (neuro)proteomics. Anal Chem. 2021;93:15964-72.

Breadmore MC, Grochocki W, Kalsoom U, Alves MN, Phung SC, Rokh MT, et al. Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2016-2018). Electrophoresis 2019;40:17-39.

Hamidli N, Andrasi M, Nagy C, Gaspar A. Analysis of intact proteins with capillary zone electrophoresis coupled to mass spectrometry using uncoated and coated capillaries. J Chromatogr A. 2021;1654:462448.

Konasova R, Butnariu M, Solinova V, Kasicka V, Koval D. Covalent cationic copolymer coatings allowing tunable electroosmotic flow for optimization of capillary electrophoretic separations. Anal Chim Acta. 2021;1178:338789.

Solinova V, Tuma P, Butnariu M, Kasicka V, Koval D. Covalent anionic copolymer coatings with tunable electroosmotic flow for optimization of capillary electrophoretic separations. Electrophoresis 2022;43:1953-62.

Roca S, Dhellemmes L, Leclercq L, Cottet H. Polyelectrolyte multilayers in capillary electrophoresis ChemPlusChem. 2022;87:e202200028.

Zhang ZB, Qu YY, Dovichi NJ. Capillary zone electrophoresis-mass spectrometry for bottom-up proteomics. Trends Anal Chem. 2018;108:23-37.

Kasicka V. Peptide mapping of proteins by capillary electromigration methods. J Sep Sci. 2022;45:4245-79.

O'Bryon I, Jenson SC, Merkley ED. Flying blind, or just flying under the radar? The underappreciated power of novo methods of mass spectrometric peptide identification. Protein Sci. 2020;29:1864-78.

Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrom Rev. 2020;39:292-306.

Noor Z, Ahn SB, Baker MS, Ranganathan S, Mohamedali A. Mass spectrometry-based protein identification in proteomics-a review. Brief Bioinform. 2021;22:1620-38.

Chen BF, Brown KA, Lin ZQ, Ge Y. Top-down proteomics: ready for prime time? Anal Chem. 2018;90:110-27.

Brown KA, Melby JA, Roberts DS, Ge Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev Proteomics 2020;17:719-33.

Wilson JW, Bilbao A, Wang J, Liao YC, Velickovic D, Wojcik R, et al. Online hydrophilic interaction chromatography (HILIC) enhanced top-down mass spectrometry characterization of the SARS-CoV-2Spike receptor-binding domain. Anal Chem. 2022;94:5909-17.

Shen XJ, Yang ZC, Mccool EN, Lubeckyj RA, Chen DY, Sun LL. Capillary zone electrophoresis-mass spectrometry for top-down proteomics. Trends Anal Chem. 2019;120:115644.

Belov AM, Zang L, Sebastiano R, Santos MR, Bush DR, Karger BL, et al. Complementary middle-down and intact monoclonal antibody proteoform characterization by capillary zone electrophoresis - mass spectrometry. Electrophoresis 2018;39:2069-82.

Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv. 2019;9:313-44.

Mehaffey MR, Xia QW, Brodbelt JS. Uniting native capillary electrophoresis and multistage ultraviolet photodissociation mass spectrometry for online separation and characterization of Escherichia coli ribosomal proteins and protein complexes. Anal Chem. 2020;92:15202-11.

Zhang WJ, Xiang Y, Xu W. Probing protein higher-order structures by native capillary electrophoresis-mass spectrometry. Trends Anal Chem. 2022;157:116739.

Rogawski R, Sharon M. Characterizing endogenous protein complexes with biological mass spectrometry. Chem Rev. 2022;122:7386-414.

Xu T, Han LJ, Sun LL. Automated capillary isoelectric focusing-mass spectrometry with ultrahigh resolution for characterizing microheterogeneity and isoelectric points of intact protein complexes. Anal Chem. 2022;94:9674-82.

Liu RJ, Xia SJ, Li HL. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. Mass Spectrom Rev. 2022;e21793.

Kumar R, Shah RL, Rathore AS. Harnessing the power of electrophoresis and chromatography: offline coupling of reverse phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry for peptide mapping for monoclonal antibodies. J Chromatogr A. 2020;1620:460954.

Kumar R, Shah RL, Ahmad S, Rathore AS. Harnessing the power of electrophoresis and chromatography: offline coupling of reverse phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry for analysis of host cell proteins in monoclonal antibody producing CHO cell line. Electrophoresis 2021;42:735-41.

Stepanova S, Kasicka V. Recent developments and applications of capillary and microchip electrophoresis in proteomic and peptidomic analyses. J Sep Sci. 2016;39:198-211.

Stepanova S, Kasicka V. Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (2015-mid 2018). J Sep Sci. 2019;42:398-414.

Ramos-Payan M, Ocana-Gonzalez JA, Fernandez-Torres RM, Llobera A, Bello-Lopez MA. Recent trends in capillary electrophoresis for complex samples analysis: A review. Electrophoresis 2018;39:111-25.

Slampova A, Mala Z, Gebauer P. Recent progress of sample stacking in capillary electrophoresis (2016-2018). Electrophoresis 2019;40:40-54.

Jarvas G, Guttman A, Miekus N, Baczek T, Jeong S, Chung DS, et al. Practical sample pretreatment techniques coupled with capillary electrophoresis for real samples in complex matrices. Trends Anal Chem. 2020;122:115702.

Martinovic T, Gajdosik MS, Josic D. Sample preparation in foodomic analyses. Electrophoresis 2018;39:1527-42.

Li YA, Qin HQ, Ye ML. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci. 2020;43:292-312.

Peng J, Zhang H, Niu H, Wu R. Peptidomic analyses: The progress in enrichment and identification of endogenous peptides. Trends Anal Chem. 2020;125:115835.

Zhang ZB, Zheng MY, Zhao YF, Wang PG. Technique development of high-throughput and high-sensitivity sample preparation and separation for proteomics. Bioanalysis 2021;14:101-11.

Thomas SL, Thacker JB, Schug KA, Marakova K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci. 2021;44:211-46.

Zheng WM, Yang PY, Sun CY, Zhang Y. Comprehensive comparison of sample preparation workflows for proteomics. Mol Omics. 2022;18:555-67.

Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, et al. Recent advances in top-down proteome sample processing ahead of MS analysis. Mass Spectrom Rev. 2023;42:457-95.

Varnavides G, Madern M, Anrather D, Hartl N, Reiter W, Hartl M. In search of a universal method: a comparative survey of bottom-up proteomics sample preparation methods. J Proteome Res. 2022;21:2397-411.

Gou MJ, Nys G, Cobraiville G, Demelenne A, Servais AC, Fillet M. Hyphenation of capillary zone electrophoresis with mass spectrometry for proteomic analysis: Optimization and comparison of two coupling interfaces. J Chromatogr A. 2020;1618:460873.

Liu SX, Li ZH, Yu B, Wang S, Shen YQ, Cong HL. Recent advances on protein separation and purification methods. Adv Colloid Interface Sci. 2020;284:102254.

El Ouahabi O, Mancera-Arteu M, Pont L, Gimenez E, Sanz-Nebot V, Benavente F. On-line solid-phase extraction to enhance sensitivity in peptide biomarker analysis by microseparation techniques coupled to mass spectrometry: Capillary liquid chromatography versus capillary electrophoresis. Microchem J. 2022;183:108089.

Sun BW, Liu ZY, Liu J, Zhao S, Wang LM, Wang FJ. The utility of proteases in proteomics, from sequence profiling to structure and function analysis. Proteomics 2022;2200132. https://doi.org/10.1002/pmic.202200132

Miller RM, Ibrahim K, Smith LM. ProteaseGuru: a tool for protease selection in bottom-up proteomics J Proteome Res. 2021;20:1936-42.

Shen XJ, Sun LL. Systematic evaluation of immobilized trypsin-based fast protein digestion for deep and high-throughput bottom-up proteomics Proteomics 2018;18:1700432.

Villegas L, Pero-Gascon R, Benavente F, Barbosa J, Sanz-Nebot V. On-line protein digestion by immobilized enzyme microreactor capillary electrophoresis-mass spectrometry. Talanta 2019;199:116-23.

Nagy C, Szabo R, Gaspar A. Microfluidic immobilized enzymatic reactors for proteomic analyses-recent developments and trends (2017-2021). Micromachines 2022;13:311.

Faserl K, Chetwynd AJ, Lynch I, Thorn JA, Lindner HH. Corona isolation method matters: capillary electrophoresis mass spectrometry based comparison of protein corona compositions following on-particle versus in-solution or in-gel digestion. Nanomaterials 2019;9:898.

Weaver SD, Schuster-Little N, Whelan RJ. Preparative capillary electrophoresis (CE) fractionation of protein digests improves protein and peptide identification in bottom-up proteomics. Anal Methods. 2022;14:1103-10.

Chen HH, Zhang LY, Zhang WB, Wang S. Construction of discontinuous capillary isoelectric focusing system and its application in pre-fractionation of exosomal proteins. Talanta 2020;208:119876.

Yang ZC, Shen XJ, Chen DY, Sun LL. Toward a universal sample preparation method for denaturing top-down proteomics of complex proteomes. J Proteome Res. 2020;19:3315-25.

Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2022;43:355-69.

Pero-Gascon R, Gimenez E, Sanz-Nebot V, Benavente F. Enrichment of histidine containing peptides by on-line immobilised metal affinity solid-phase extraction capillary electrophoresis-mass spectrometry. Microchem J. 2020;157:105013.

Li YL, Sun NR, Hu XF, Li Y, Deng CH. Recent advances in nanoporous materials as sample preparation techniques for peptidome research. Trends Anal Chem. 2019;120:115658.

Irfan A, Feng WX, Liu KX, Habib K, Qu Q, Yang L. TiO2-modified fibrous core-shell mesoporous material to selectively enrich endogenous phosphopeptides with proteins exclusion prior to CE-MS analysis. Talanta 2021;235:122737.

Yang ZC, Sun LL. Recent technical progress in sample preparation and liquid-phase separation-mass spectrometry for proteomic analysis of mass-limited samples. Anal Methods. 2021;13:1214-25.

Lubeckyj RA, Sun LL. Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain. Mol Omics. 2022;18:112-22.

Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, et al. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019;19:1800361.

Baghalabadi V, Doucette AA. Mass spectrometry profiling of low molecular weight proteins and peptides isolated by acetone precipitation. Anal Chim Acta. 2020;1138:38-48.

Vissers JPC, McCullagh M. An analytical perspective on protein analysis and discovery proteomics by ion mobility-mass spectrometry. Methods Mol Biol. 2020;2084:161-78.

Messner CB, Demichev V, Wang ZY, Hartl J, Kustatscher G, Muelleder M, et al. Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology. Proteomics 2022;2200013. https://doi.org/10.1002/pmic.202200013

Gargano AFG, Roca LS, Fellers RT, Bocxe M, Dominguez-Vega E, Somsen GW. Capillary HILIC-MS: a new tool for sensitive top-down proteomics Anal Chem. 2018;90:6601-9.

Piovesana S, Cerrato A, Antonelli M, Benedetti B, Capriotti AL, Cavaliere C, et al. A clean-up strategy for identification of circulating endogenous short peptides in human plasma by zwitterionic hydrophilic liquid chromatography and untargeted peptidomics identification. J Chromatogr A. 2020;1613:460699.

Martelli C, Desiderio C. Capillary electrophoresis-mass spectrometry for proteomics, in: Poole CF, editor. Capillary electromigration separation methods. Amsterdam: Elsevier Science Bv; 2018. pp. 335-51.

Gomes FP, Yates III. Recent trends of capillary electrophoresis-mass spectrometry in proteomics research. Mass Spectrom Rev. 2019;38:445-60.

Kuzyk VO, Somsen GW, Haselberg R. CE-MS for proteomics and intact protein analysis, in: Simionato AVC, editor. Separation techniques applied to omics sciences: from principles to relevant applications. Cham: Springer International Publishing Ag; 2021. pp. 51-86.

Shah U, Patel A, Patel R, Patel M, Patel A, Kavad M, et al. Overview on capillary electrophoresis with mass spectrometry: Application in peptide analysis and proteomics. Int J Pharm Chem Anal. 2021;8:6-15.

Yan XJ, Sun LL, Dovichi NJ, Champion MM. Minimal deuterium isotope effects in quantitation of dimethyl-labeled complex proteomes analyzed with capillary zone electrophoresis/mass spectrometry. Electrophoresis 2020;41:1374-8.

Wu HM, Tang KQ. Highly sensitive and robust capillary electrophoresis-electrospray ionization-mass spectrometry: interfaces, preconcentration techniques and applications. Rev Anal Chem. 2020;39:45-55.

Schlecht J, Stolz A, Hofmann A, Gerstung L, Neususs C. nanoCEasy: an easy, flexible, and robust nanoflow sheath liquid capillary electrophoresis-mass spectrometry interface based on 3D printed parts. Anal Chem. 2021;93:14593-8.

Wang LY, Bo T, Zhang ZX, Wang GB, Tong WJ, Chen DD. High resolution capillary isoelectric focusing mass spectrometry analysis of peptides, proteins, and monoclonal antibodies with a flow-through microbial interface. Anal Chem. 2018;90:9495-503.

Romson J, Jacksen J, Emmer A. An automated system for CE-MALDI and on-target digestion under a fluorocarbon lid applied on spermatophore proteins from Pieris napi. J Chromatogr B. 2019;1104:228-33.

DeLaney K, Li LJ. Capillary electrophoresis coupled to MALDI mass spectrometry imaging with large volume sample stacking injection for improved coverage of C. borealis neuropeptidome. Analyst 2020;145:61-9.

Romer J, Stolz A, Kiessig S, Moritz B, Neususs C. Online top-down mass spectrometric identification of CE(SDS)-separated antibody fragments by two-dimensional capillary electrophoresis. J Pharm Biomed Anal. 2021;201:114089.

Qu YY, Sun LL, Zhang ZB, Dovichi NJ. Site-specific glycan heterogeneity characterization by hydrophilic interaction liquid chromatography solid-phase extraction, reversed-phase liquid chromatography fractionation, and capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry. Anal Chem. 2018;90:1223-33.

Yang ZC, Shen XJ, Chen DY, Sun LL. Improved nanoflow RPLC-CZE-MS/MS system with high peak capacity and sensitivity for nanogram bottom-up proteomics. J Proteome Res. 2019;18:4046-54.

Jooss K, Scholz N, Meixner J, Neususs C. Heart-cut nano-LC-CZE-MS for the characterization of proteins on the intact level. Electrophoresis 2019;40:1061-5.

Stolz A, Neususs C. Characterisation of a new online nanoLC-CZE-MS platform and application for the glycosylation profiling of alpha-1-acid glycoprotein. Anal Bioanal Chem. 2022;414:1745-57.

Lazar IM, Gulakowski NS, Lazar AC. Protein and proteome measurements with microfluidic chips. Anal Chem. 2020;92:169-82.

Shao XY, Huang YY, Wang GB. Microfluidic devices for protein analysis using intact and top-down mass spectrometry. View. 2022;20220032. https://doi.org/10.1002/VIW.20220032

Vitorino R, Guedes S, da Costa JP, Kasicka V. Microfluidics for peptidomics, proteomics, and cell analysis. Nanomaterials 2021;11:1118.

Ou XW, Chen P, Huang XZ, Li SJ, Liu BF. Microfluidic chip electrophoresis for biochemical analysis. J Sep Sci. 2020;43:258-70.

Chen P, Chen DJ, Li SJ, Ou XW, Liu BF. Microfluidics towards single cell resolution protein analysis. Trends Anal Chem. 2019;117:2-12.

Miller RM, Smith LM. Overview and considerations in bottom-up proteomics. Analyst 2023; 148:475-486. https://doi.org/10.1039/d2an01246d

Zhang ZB, Hebert AS, Westphall MS, Qu YY, Coon JJ, Dovichi NJ. 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. Anal Chem. 2018;90:12090-3.

Johnson KR, Gregus M, Ivanov AR. Coupling high-field asymmetric ion mobility spectrometry with capillary electrophoresis-electrospray ionization-tandem mass spectrometry improves protein identifications in bottom-up proteomic analysis of low nanogram samples. J Proteome Res. 2022;21:2453-61.

Chen DY, Ludwig KR, Krokhin OV, Spicer V, Yang ZC, Shen XJ, et al. 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. Anal Chem. 2019;91:2201-8.

Cheng JH, Morin GB, Chen DDY. Bottom-up proteomics of envelope proteins extracted from spinach chloroplast via high organic content CE-MS. Electrophoresis 2020;41:370-8.

Tsuchiya T, Nakayama A, Kawamura T, Sasaki K. Capillary electrophoresis electrospray ionization-mass spectrometry for peptidomics-based processing site determination. Biochem Biophys Res Commun. 2020;533:872-8.

Cheng JH, Wang LY, Rive CM, Holt RA, Morin GB, Chen DDY. Complementary methods for de Novo monoclonal antibody sequencing to achieve complete sequence coverage. J Proteome Res. 2020;19:2700-7.

Gou MJ, Kose MC, Crommen J, Nix C, Cobraiville G, Caers J, et al. Contribution of capillary zone electrophoresis hyphenated with drift tube ion mobility mass spectrometry as a complementary tool to microfluidic reversed phase liquid chromatography for antigen discovery. Int J Mol Sci. 2022;23:13350.

Ali F, Alothman ZA, Al-Shaalan NH. Mixed-mode open tubular column for peptide separations by capillary electrochromatography. J Sep Sci. 2021;44:2602-11.

Nagy C, Andrasi M, Hamidli N, Gyemant G, Gaspar A. Top-down proteomic analysis of monoclonal antibodies by capillary zone electrophoresis-mass spectrometry. J Chromatogr Open. 2022;2:100024.

Mccool EN, Lubeckyr R, Shen XJ, Kou Q, Liu XW, Sun LL. Large-scale top-down proteomics using capillary zone electrophoresis tandem mass spectrometry. Jove-J Visual Exp. 2018;e58644.

Mccool EN, Sun LL. Comparing nanoflow reversed-phase liquid chromatography-tandem mass spectrometry and capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics. Chin J Chromatogr. 2019;37:878-86.

Meyer S, Clases D, de Vega RG, Padula MP, Doble PA. Separation of intact proteins by capillary electrophoresis. Analyst 2022;147:2988-96.

Wang TT, Chen DY, Lubeckyj RA, Shen XJ, Yang ZC, Mccool EN, et al. Capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics using attapulgite nanoparticles functionalized separation capillaries. Talanta 2019;202:165-70.

Johnson KR, Gao YF, Gregus M, Ivanov AR. On-capillary cell lysis enables top-down proteomic analysis of single mammalian cells by CE-MS/MS. Anal Chem. 2022;94:14358-67.

Chen DY, Lubeckyj RA, Yang ZC, Mccool EN, Shen XJ, Wang QJ, et al. Predicting electrophoretic mobility of proteoforms for large-scale top-down proteomics. Anal Chem. 2020;92:3503-7.

Chen WR, Mccool EN, Sun LL, Zang Y, Ning X, Liu XW. Evaluation of machine learning models for proteoform retention and migration time prediction in top-down mass spectrometry. J Proteome Res. 2022;21:1736-47.

Mccool EN, Lodge JM, Basharat AR, Liu XW, Coon JJ, Sun LL. Capillary zone electrophoresis-tandem mass spectrometry with activated ion electron transfer dissociation for large-scale top-down proteomics. J Am Soc Mass Spectrom. 2019;30:2470-9.

Shen XJ, Xu T, Hakkila B, Hare M, Wang QJ, Wang QY, et al. Capillary zone electrophoresis-electron-capture collision-induced dissociation on a quadrupole time-of-flight mass spectrometer for top-down characterization of intact proteins. J Am Soc Mass Spectrom. 2021;32:1361-9.

Gomes FP, Diedrich JK, Saviola AJ, Memili E, Moura AA, Yates JR. EThcD and 213 nm UVPD for top-down analysis of bovine seminal plasma proteoforms on electrophoretic and chromatographic time frames. Anal Chem. 2020;92:2979-87.

Liu RD, Cheddah S, Liu SQ, Liu YY, Wang Y, Yan C. A porous layer open-tubular capillary column with immobilized pH gradient (PLOT-IPG) for isoelectric focusing of amino acids and proteins. Anal Chim Acta. 2019;1048:204-11.

Xu T, Shen XJ, Yang ZC, Chen DY, Lubeckyj RA, Mccool EN, et al. Automated capillary isoelectric focusing-tandem mass spectrometry for qualitative and quantitative top-down proteomics. Anal Chem. 2020;92:15890-8.

Camperi J, Pichon V, Delaunay N. Separation methods hyphenated to mass spectrometry for the characterization of the protein glycosylation at the intact level. J Pharm Biomed Anal. 2020;178:112921.

Molnarova K, Cokrtova K, Tomnikova A, Krizek T, Kozlik P. Liquid chromatography and capillary electrophoresis in glycomic and glycoproteomic analysis. Monatshefte fur Chemie. 2022;153:659-86.

Zhang ZB, Hebert AS, Westphall MS, Coon JJ, Dovichi NJ. Single-shot capillary zone electrophoresis-tandem mass spectrometry produces over 4400 phosphopeptide identifications from a 220 ng sample. J Proteome Res. 2019;18:3166-73.

Pont L, Kuzyk V, Benavente F, Sanz-Nebot V, Mayboroda OA, Wuhrer M, et al. Site-Specific N-Linked Glycosylation Analysis of Human Carcinoembryonic Antigen by Sheathless Capillary Electrophoresis-Tandem Mass Spectrometry. J Proteome Res. 2021;20:1666-75.

Mccool EN, Chen DY, Li WX, Liu YS, Sun LL. Capillary zone electrophoresis-tandem mass spectrometry with ultraviolet photodissociation (213 nm) for large-scale top-down proteomics. Anal Methods. 2019;11:2855-61.

Lombard-Banek C, Moody SA, Manzin MC, Nemes P. Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos. Anal Chem. 2019;91:4797-805.

Choi SB, Polter AM, Nemes P. Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry. Anal Chem. 2022;94:1637-44.

Chen DY, Yang ZC, Shen XJ, Sun LL. Capillary Zone Electrophoresis-Tandem Mass Spectrometry As an Alternative to Liquid Chromatography-Tandem Mass Spectrometry for Top-down Proteomics of Histones. Anal Chem. 2021;93:4417-24.

Bosso M, Standker L, Kirchhoff F, Munch J. Exploiting the human peptidome for novel antimicrobial and anticancer agents. Bioorg Med Chem. 2018;26:2719-26.

Maes E, Oeyen E, Boonen K, Schildermans K, Mertens I, Pauwels P, et al. The challenges of peptidomics in complementing proteomics in a clinical context. Mass Spectrom Rev. 2019;38:253-64.

Vitorino R. Digging Deep into Peptidomics Applied to Body Fluids. Proteomics 2018;18:1700401.

Foreman RE, George AL, Reimann F, Gribble FM, Kay RG. Peptidomics: A Review of Clinical Applications and Methodologies. J Proteome Res. 2021;20:3782-97.

Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE-MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019;40:2294-308.

Krochmal M, Schanstra JP, Mischak H. Urinary peptidomics in kidney disease and drug research. Expert Opin Drug Discov. 2018;13:259-68.

Persson F, Rossing P. Urinary Proteomics and Precision Medicine for Chronic Kidney Disease: Current Status and Future Perspectives. Proteomics Clin Appl. 2019;13:1800176.

Belczacka I, Pejchinovski M, Krochmal M, Magalhaes P, Frantzi M, Mullen W, et al. Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers. Proteomics Clin Appl. 2019;13:1800111.

Lucas-Herald AK, Zurbig P, Mason A, Kinning E, Brown CE, Mansoorian B, et al. Proteomic evidence of biological aging in a child with a compound heterozygous ZMPSTE24 mutation. Proteomics Clin Appl. 2019;13:1800135.

Sirolli V, Pieroni L, Di Liberato L, Urbani A, Bonomini M. Urinary peptidomic biomarkers in kidney diseases. Int J Mol Sci. 2020;21:96.

Latosinska A, Siwy J, Faguer S, Beige J, Mischak H, Schanstra JP. Value of urine peptides in assessing kidney and cardiovascular disease. Proteomics Clin Appl. 2021;15:2000027.

Rodriguez-Ortiz ME, Pontillo C, Rodriguez M, Zurbig P, Mischak H, Ortiz A. Novel urinary biomarkers for improved prediction of progressive Egfr loss in early chronic kidney disease stages and in high risk individuals without chronic kidney disease. Sci Rep. 2018;8:15940.

Pelander L, Brunchault V, Buffin-Meyer B, Klein J, Breuil B, Zurbig P, et al. Urinary peptidome analyses for the diagnosis of chronic kidney disease in dogs. Vet J. 2019;249:73-9.

Wendt R, Siwy J, He TL, Latosinska A, Wiech T, Zipfel PF, et al. Molecular mapping of urinary complement peptides in kidney diseases. Proteomes 2021;9:49.

Rudnicki M, Siwy J, Wendt R, Lipphardt M, Koziolek MJ, Maixnerova D, et al. Urine proteomics for prediction of disease progression in patients with IgA nephropathy. Nephrol Dial Transplant. 2022;37:42-52.

Rambabova-Bushljetik I, Metzger J, Siwy J, Dohcev S, Bushljetikj O, Filipce V, et al. Association of the chronic kidney disease urinary proteomic predictor CKD273 with clinical risk factors of graft failure in kidney allograft recipients. Nephrol Dial Transplant. 2022;37:2014-21.

Kanzelmeyer NK, Zurbig P, Mischak H, Metzger J, Fichtner A, Ruszai KH, et al. Urinary proteomics to diagnose chronic active antibody-mediated rejection in pediatric kidney transplantation - a pilot study. Transplant Int. 2019;32:28-37.

Marx D, Metzger J, Olagne J, Belczacka I, Faguer S, Colombat M, et al. Proteomics in kidney allograft transplantation-application of molecular pathway analysis for kidney allograft disease phenotypic biomarker selection. Proteomics Clin Appl. 2019;13:1800091.

Zhang ZY, Nkuipou-Kenfack E, Yang WY, Wei FF, Cauwenberghs N, Thijs L, et al. Epidemiologic observations guiding clinical application of a urinary peptidomic marker of diastolic left ventricular dysfunction. J Am Soc Hypertension. 2018;12:438-47.

Campbell RT, Jasilek A, Mischak H, Nkuipou-Kenfack E, Latosinska A, Welsh PI, et al. The novel urinary proteomic classifier HF1 has similar diagnostic and prognostic utility to BNP in heart failure. Esc Heart Failure. 2020;7:1595-604.

Wei DM, Melgarejo JD, Thijs L, Temmerman X, Vanassche T, Van Aelst L, et al. Urinary proteomic profile of arterial stiffness is associated with mortality and cardiovascular outcomes. J Am Heart Assoc. 2022;11:e024769.

Nicol K, Mansoorian B, Latosinska A, Koutroulaki A, Mullen B, Combet E. No evidence of differential impact of sunflower and rapeseed oil on biomarkers of coronary artery disease or chronic kidney disease in healthy adults with overweight and obesity: result from a randomised control trial. Eur J Nutr. 2022;61:3119-33.

Bannaga A, Metzger J, Voigtlander T, Pejchinovski M, Frantzi M, Book T, et al. Pathophysiological implications of urinary peptides in hepatocellular carcinoma. Cancers 2021;13:3786.

Tailliar M, Schanstra JP, Dierckx T, Breuil B, Hanouna G, Charles N, et al. Urinary peptides as potential non-invasive biomarkers for lupus nephritis: results of the peptidu-LUP study. J Clin Med. 2021;10:1690.

Bannaga AS, Metzger J, Kyrou I, Voigtlander T, Book T, Melgarejo J, et al. Discovery, validation and sequencing of urinary peptides for diagnosis of liver fibrosis-A multicentre study. Ebiomedicine 2020;62:103083.

Staessen JA, Wendt R, Yu YL, Kalbitz S, Thijs L, Siwy J, et al. Predictive performance and clinical application of COV50, a urinary proteomic biomarker in early COVID-19 infection: a prospective multicentre cohort study. Lancet Digital Health. 2022;4:E727-37.

Ricci P, Magalhaes P, Krochmal M, Pejchinovski M, Daina E, Caruso MR, et al. Urinary proteome signature of Renal Cysts and Diabetes syndrome in children. Sci Rep. 2019;9:2225.

Nkuipou-Kenfack E, Latosinska A, Yang WY, Fournier MC, Blet A, Mujaj B, et al. A novel urinary biomarker predicts 1-year mortality after discharge from intensive care. Critical Care. 2020;24:10.

Omar M, Windhagen H, Krettek C, Ettinger M. Noninvasive diagnostic of periprosthetic joint infection by urinary peptide markers: a preliminary study. J Orthop Res. 2021;39:339-47.

Mavrogeorgis E, Mischak H, Latosinska A, Siwy J, Jankowski V, Jankowski J. Reproducibility evaluation of urinary peptide detection using CE-MS. Molecules 2021;26:7260.

Magalhaes P, Pontillo C, Pejchinovski M, Siwy J, Krochmal M, Makridakis M, et al. Comparison of urine and plasma peptidome indicates selectivity in renal peptide handling. Proteomics Clin Appl. 2018;12:1700163.

He TL, Pejchinovski M, Mullen W, Beige J, Mischak H, Jankowski V. Peptides in plasma, urine, and dialysate: toward unravelling renal peptide handling. Proteomics Clin Appl. 2021;15:2000029.

Catanese L, Siwy J, Mavrogeorgis E, Amann K, Mischak H, Beige J, et al. A novel urinary proteomics classifier for non-invasive evaluation of interstitial fibrosis and tubular atrophy in chronic kidney disease. Proteomes 2021;9:32.

Wendt R, Kalbitz S, Lubbert C, Kellner N, Macholz M, Schroth S, et al. Urinary peptides significantly associate with COVID-19 severity: pilot proof-of-principle data and design of a multicentric diagnostic study. Proteomics 2020;20:2000202.

Wendt R, Thijs L, Kalbitz S, Mischak H, Siwy J, Raad J, et al. A urinary peptidomic profile predicts outcome in SARS-CoV-2-infected patients. Eclinicalmedicine 2021;36:100883.

Moran AB, Dominguez-Vega E, Nouta J, Pongracz T, de Reijke TM, Wuhrer M, et al. Profiling the proteoforms of urinary prostate-specific antigen by capillary electrophoresis - mass spectrometry. J Proteomics 2021;238:104148.

Stolz A, Hedeland Y, Salzer L, Romer J, Heiene R, Leclercq L, et al. Capillary zone electrophoresis-top-down tandem mass spectrometry for in-depth characterization of hemoglobin proteoforms in clinical and veterinary samples. Anal Chem. 2020;92:10531-9.

Luo RY, Wong C, Xia JQ, Glader BE, Shi RZ, Zehnder JL. Neutral-coating capillary electrophoresis coupled with high-resolution mass spectrometry for top-down identification of hemoglobin variants. Clin Chem. 2023;69:56-67.

Jiang JL, Zhan LP, Dai LY, Yao XP, Qin Y, Zhu ZQ, et al. Evaluation of the reliability of MS1-based approach to profile naturally occurring peptides with clinical relevance in urine samples. Rapid Commun Mass Spectrom. 2022;9999:e9369.

Michalusova I, Sazelova P, Cejnar P, Kuckova S, Hynek R, Kasicka V. Capillary electrophoretic profiling of in-bone tryptic digests of proteins as a potential tool for the detection of inflammatory states in oral surgery. J Sep Sci. 2020;43:3949-59.

Lombard-Banek C, Yu Z, Swiercz AP, Marvar PJ, Nemes P. A microanalytical capillary electrophoresis mass spectrometry assay for quantifying angiotensin peptides in the brain. Anal Bioanal Chem. 2019;411:4661-71.

Guzman NA, Guzman DE. A two-dimensional affinity capture and separation mini-platform for the isolation, enrichment, and quantification of biomarkers and its potential use for liquid biopsy. Biomedicines 2020;8:255.

Guzman NA, Guzman DE. Immunoaffinity capillary electrophoresis in the era of proteoforms, liquid biopsy and preventive medicine: a potential impact in the diagnosis and monitoring of disease progression. Biomolecules 2021;11:1443.

Toldra F, Reig M, Aristoy MC, Mora L. Generation of bioactive peptides during food processing. Food Chem. 2018;267:395-404.

Li X, Gu YX, He SD, Dudu OE, Li QM, Liu HY, et al. Influence of pasteurization and storage on dynamic in vitro gastric digestion of milk proteins: quantitative insights based on peptidomics. Foods 2020;9:998.

Renzone G, Novi G, Scaloni A, Arena S. Monitoring aging of hen egg by integrated quantitative peptidomic procedures. Food Res Int. 2021;140:110010.

Vreeke GJC, Lubbers W, Vincken JP, Wierenga PA. A method to identify and quantify the complete peptide composition in protein hydrolysates. Anal Chim Acta. 2022;1201:339616.

Agyei D, Tsopmo A, Udenigwe CC. Bioinformatics and peptidomics approaches to the discovery and analysis of food-derived bioactive peptides. Anal Bioanal Chem. 2018;410:3463-72.

Punia H, Tokas J, Malik A, Sangwan S, Baloda S, Singh N, et al. Identification and detection of bioactive peptides in milk and dairy products: remarks about agro-foods. Molecules 2020;25:3328.

Arena S, Renzone G, Scaloni A. A multi-approach peptidomic analysis of hen egg white reveals novel putative bioactive molecules. J Proteomics 2020;215:103646.

Abril AG, Pazos M, Villa TG, Calo-Mata P, Barros-Velazquez J, et al. Proteomics characterization of food-derived bioactive peptides with anti-allergic and anti-inflammatory properties. Nutrients. 2022;14:4400.

Gan JN, Robinson RC, Wang JQ, Krishnakumar N, Manning CJ, Lor Y, et al. Peptidomic profiling of human milk with LC-MS/MS reveals pH-specific proteolysis of milk proteins. Food Chem. 2019;274:766-74.

Agregan R, Echegaray N, Lopez-Pedrouso M, Kharabsheh R, Franco D, Lorenzo JM. Proteomic advances in milk and dairy products. Molecules 2021;26:3832.

Ten-Domenech I, Simo-Alfonso EF, Herrero-Martinez JM. Improving fractionation of human milk proteins through calcium phosphate coprecipitation and their rapid characterization by capillary electrophoresis. J Proteome Res. 2018;17:3557-64.

Trimboli F, Costanzo N, Lopreiato V, Ceniti C, Morittu VM, Spina A, et al. Detection of buffalo milk adulteration with cow milk by capillary electrophoresis analysis. J Dairy Sci. 2019;102:5962-70.

Masci M, Zoani C, Nevigato T, Turrini A, Jasionowska R, Caproni R, et al. Authenticity assessment of dairy products by capillary electrophoresis. Electrophoresis 2022;43:340-54.

Ghafoori Z, Tehrani T, Pont L, Benavente F. Separation and characterization of bovine milk proteins by capillary electrophoresis-mass spectrometry. J Sep Sci. 2022;45:3614-27.

Benavente F, Pero-Gascon R, Pont L, Jaumot J, Barbosa J, Sanz-Nebot V. Identification of antihypertensive peptides in nutraceuticals by capillary electrophoresis-mass spectrometry. J Chromatogr A. 2018;1579:129-37.

Find record

Citation metrics

Loading data ...

Archiving options

Loading data ...