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

Zhu, Guijie; Sun, Liangliang; Yan, Xiaojing; Dovichi, Norman J.

doi:10.1021/ac303750g

Cited by 103Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMicrofluidic and Capillary Electrophoresis Applications

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

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Zhu, Guijie, Sun, Liangliang, Yan, Xiaojing, Dovichi, Norman J.·2013·Analytical Chemistry

DOI 10.1021/ac303750gPMC PMC3594080

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Abstract

Capillary zone electrophoresis (CZE)-electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was optimized and applied for analysis of 1-100 ng Escherichia coli protein digests in a single run (single-shot analysis). The system employed an electrokinetically pumped nanospray interface, a coated capillary, and stacking conditions for sample injection. More than 1 250 peptides were identified by optimized single-shot CZE-ESI-MS/MS with 100 ng digest loaded and 50 min analysis time. When 10 ng and 1 ng digests were loaded, about 1 000 and 600 peptides were identified in a single-shot analysis, respectively. Compared with single-shot ultraperformance liquid chromatography (UPLC)-ESI-MS/MS, CZE-ESI-MS/MS produced fewer peptide IDs (1 377 ± 128 vs 1 875 ± 32) for large sample loading amounts (100 ng) with the same mass spectrometer time (50 min). However, when the loaded digest was mass limited (1 ng), CZE-ESI-MS/MS generated many more peptide identifications than UPLC-ESI-MS/MS (627 ± 38 vs 342 ± 113). In addition, CZE-ESI-MS/MS and UPLC-ESI -MS/MS provided complementary peptide level identifications. These results suggest that CZE-ESI-MS/MS may be useful for large-scale, comprehensive, and confident proteomics analysis.

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Many studies have suggested that CZE separations are more capable of identifying hydrophilic peptides than LC.
“Many studies have suggested that CZE separations are more capable of identifying hydrophilic peptides than LC48,87.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [48]

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Authors: Zhu, G., Sun, L., Yan, X., & 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: Sun, Liangliang
Yan, Xiaojing
Venue: Analytical Chemistry
Publisher: American Chemical Society (ACS)
Published: 2013-02-13
Volume: 85
Issue: 5
Pages: 2569-2573
ISSN: 0003-2700 (ISSN-L)
1520-6882
DOI: 10.1021/ac303750g
PMC: PMC3594080
OpenAlex: W1982607050
Cited by: 103
References: 24
Citations by year: 2026: 2 · 2025: 3 · 2024: 3 · 2023: 2 · 2022: 3 · 2021: 5 · 2020: 5 · 2019: 7 · 2018: 9 · 2017: 12 · 2016: 6 · 2015: 15 · 2014: 15 · 2013: 15 · 2012: 1
FWCI: 7.64
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: Analytical Chemistry (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institutes of Health
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: capillary zone electrophoresis, electrospray ionization, tandem mass spectrometry, Escherichia coli, peptide identification, coated capillaries, sample stacking, protein digests
MeSH terms: Chromatography, High Pressure Liquid, Peptide Fragments, Time Factors, Electrophoresis, Capillary, Spectrometry, Mass, Electrospray Ionization, Escherichia coli Proteins, Proteomics, Tandem Mass Spectrometry, Proteolysis

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

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