Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome
Open accessAbstract
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as a useful tool for top-down proteomics. However, its performance for deep top-down proteomics is still dramatically lower than widely used reversed-phase liquid chromatography (RPLC)-MS/MS. We present an orthogonal multidimensional separation platform that couples size exclusion chromatography (SEC) and RPLC based protein prefractionation to CZE-MS/MS for deep top-down proteomics of Escherichia coli. The platform generated high peak capacity (∼4000) for separation of intact proteins, leading to the identification of 5700 proteoforms from the Escherichia coli proteome. The data represents a 10-fold improvement in the number of proteoform identifications compared with previous CZE-MS/MS studies and represents the largest bacterial top-down proteomics data set reported to date. The performance of the CZE-MS/MS based platform is comparable to the state-of-the-art RPLC-MS/MS based systems in terms of the number of proteoform identifications and the instrument time.
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SEC coupled to CZE identified ~5700 proteoforms from E. coli.
“SEC was also coupled to CZE for the identification of ~5700 proteoforms from Escherichia coli [86].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [86]
High peak capacity and resolving power improved data acquisition and enhanced representation of proteins in the sample.
“High peak capacity and resolving power improved the data acquisition, which resulted in an enhanced representation of the proteins in the sample.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [51]
McCool and co-workers demonstrated orthogonal multidimensional separation for a large-scale top-down study that identified 850 proteins and 5700 proteoforms from Escherichia coli.
“McCool and co-workers demonstrated the value of orthogonal multidimensional separation for a large-scale top-down study that identified 850 proteins and 5700 proteoforms from Escherichia coli51.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [51]
This platform resulted in a peak capacity of about 4,000 for separation of intact proteins.
“This platform resulted in a peak capacity of ~4,000 for separation of intact proteins.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [51]
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Self-citation
- Authors
- McCool, E. N., Lubeckyj, R. A., Shen, X., Chen, D., Kou, Q., Liu, X., & Sun, L.
- Affiliations
- Michigan State University (US)
- Indiana University Indianapolis (US)
- Corresponding author
- Sun, Liangliang
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-04-05
- Volume
- 90
- Issue
- 9
- Pages
- 5529-5533
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC5930140
- OpenAlex
- W2796143940
- Cited by
- 117
- References
- 39
- Citations by year
- 2026: 10 · 2025: 9 · 2024: 4 · 2023: 14 · 2022: 15 · 2021: 13 · 2020: 20 · 2019: 20 · 2018: 12
- 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)
- PMC
- Funders
- National Institute of General Medical Sciences (R01GM118470, R01GM125991)
- 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, tandem mass spectrometry, Escherichia coli proteome, proteoforms, size exclusion chromatography, intact protein separation, peak capacity
- MeSH terms
- Escherichia coli, Electrophoresis, Capillary, Proteome, Escherichia coli Proteins, Proteomics, Tandem Mass Spectrometry
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