Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography–Capillary Zone Electrophoresis–Tandem Mass Spectrometry
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Native proteomics aims to characterize complex proteomes under native conditions and ultimately produces a full picture of endogenous protein complexes in cells. It requires novel analytical platforms for high-resolution and liquid-phase separation of protein complexes prior to native mass spectrometry (MS) and MS/MS. In this work, size-exclusion chromatography (SEC)-capillary zone electrophoresis (CZE)-MS/MS was developed for native proteomics in discovery mode, resulting in the identification of 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome. The protein complexes include four protein homodimers, 16 protein-metal complexes, two protein-[2Fe-2S] complexes, and one protein-glutamine complex. Half of them have not been reported in the literature. This work represents the first example of online liquid-phase separation-MS/MS for the characterization of a complex proteome under the native condition, offering the proteomics community an efficient and simple platform for native proteomics.
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Native SEC and CZE coupled identified 672 proteoforms, 144 proteins, and 23 protein complexes.
“For example, native SEC and CZE were coupled to identify 672 proteoforms, 144 proteins, and 23 protein complexes [88].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [88]
Shen and co-workers successfully used an aqueous 25 mM ammonium acetate sheath-liquid for analysis of protein complexes from Escherichia coli.
“Shen and co-workers successfully applied an aqueous solution of 25mM ammonium acetate as a sheath-liquid for the analysis of protein complexes from Escherichia coli21.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [21]
Because CE separations can be performed in aqueous buffers, protein complexes can be separated in native structures, preserving non-covalent interactions before MS detection.
“Since CE separations can be performed in aqueous buffers, protein complexes can be separated in their native structures, preserving non-covalent interactions within a protein and between subunits of protein assemblies, prior to MS detection19–21.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [21]
Shen and co-workers demonstrated SEC-CZE for analysis of protein complexes and proteoforms under near native conditions, identifying 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome.
“More recently, Shen and co-workers demonstrated the use of SEC-CZE for analysis of protein complexes and proteoforms under near native conditions21, resulting in the identification of 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [21]
High-throughput native separation techniques including GELFrEE, HIC, SEC, CZE, and IEX have efficiently aided in the analysis of heterogeneous protein mixtures.
“Recently, high-throughput native separation techniques including GELFrEE,36 HIC,39,40 SEC,112 capillary zone electrophoresis (CZE),112 and IEX38 have efficiently aided in the analysis of heterogeneous protein mixtures.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [112]
Sun and co-workers showed that SEC and CZE can separate multiple proteins and protein complexes before analysis with complex-down mass spectrometry on a lysate of E. coli, resulting in identification of 672 proteoforms and 23 protein complexes.
“In a different example, Sun and co-workers showed that SEC and CZE can separate multiple proteins and protein complexes before analysis with complex-down mass spectrometry on a lysate of E. coli, resulting in the identification of 672 proteoforms and 23 protein complexes.112”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [112]
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- Authors
- Shen, X., Kou, Q., Guo, R., Yang, Z., Chen, D., Liu, X., Hong, H., & Sun, L.
- Affiliations
- Michigan State University (US)
- Indiana University – Purdue University Indianapolis (US)
- Indiana University Indianapolis (US)
- Corresponding author
- Sun, Liangliang
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-08-07
- Volume
- 90
- Issue
- 17
- Pages
- 10095-10099
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC6156775
- OpenAlex
- W2885135849
- Cited by
- 78
- References
- 46
- Citations by year
- 2026: 6 · 2025: 10 · 2024: 10 · 2023: 6 · 2022: 12 · 2021: 11 · 2020: 11 · 2019: 10 · 2018: 2
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Purdue University Indianapolis (Indiana University) (submittedVersion)
- Author eBooks
- Funders
- National Institute of General Medical Sciences (R01GM118470, R01GM125991, R01GM118685)
- 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
- protein complexes, size exclusion chromatography, capillary zone electrophoresis, tandem mass spectrometry, Escherichia coli proteome, protein homodimer, protein-metal complex, proteoforms
- MeSH terms
- Chromatography, Gel, Electrophoresis, Capillary, Escherichia coli Proteins, Proteomics, Tandem Mass Spectrometry
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