Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry as an Alternative Proteomics Platform to Ultraperformance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry for Samples of Intermediate Complexity

Li, Yihan; Champion, Matthew M.; Sun, Liangliang; Champion, Patricia A. DiGiuseppe; Wojcik, Roza; Dovichi, Norman J.

doi:10.1021/ac202899p

Cited by 128Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMicrofluidic and Capillary Electrophoresis Applications

Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry as an Alternative Proteomics Platform to Ultraperformance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry for Samples of Intermediate Complexity

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Li, Yihan, Champion, Matthew M., Sun, Liangliang, Champion, Patricia A. DiGiuseppe, Wojcik, Roza, Dovichi, Norman J.·2012·Analytical Chemistry

DOI 10.1021/ac202899pPMC PMC3277681

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Abstract

We demonstrate the use of capillary zone electrophoresis with an electrokinetically pumped sheath-flow electrospray interface for the analysis of a tryptic digest of a sample of intermediate protein complexity, the secreted protein fraction of Mycobacterium marinum. For electrophoretic analysis, 11 fractions were generated from the sample using reverse-phase liquid chromatography; each fraction was analyzed by CZE-ESI-MS/MS, and 334 peptides corresponding to 140 proteins were identified in 165 min of mass spectrometer time at 95% confidence (FDR < 0.15%). In comparison, 388 peptides corresponding to 134 proteins were identified in 180 min of mass spectrometer time by triplicate UPLC-ESI-MS/MS analyses, each using 250 ng of the unfractionated peptide mixture, at 95% confidence (FDR < 0.15%). Overall, 62% of peptides identified in CZE-ESI-MS/MS and 67% in UPLC-ESI-MS/MS were unique. CZE-ESI-MS/MS favored basic and hydrophilic peptides with low molecular masses. Combining the two data sets increased the number of unique peptides by 53%. Our approach identified more than twice as many proteins as the previous record for capillary electrophoresis proteome analysis. CE-ESI-MS/MS is a useful tool for the analysis of proteome samples of intermediate complexity.

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Li and co-workers reported a bottom-up strategy combining CZE-MS and reversed-phase LC-MS data, which improved the number of identified unique peptides, with hydrophilic and basic low-molecular-weight peptides predominantly identified by CZE-MS.
“For instance, Li and co-workers reported a bottom-up strategy that combines the data from CZE-MS and reversed-phase LC-MS91. This combination resulted in an improved number of identified unique peptides where hydrophilic and basic peptides with low molecular weight were predominantly identified via CZE-MS.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [91]

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Authors: Li, Y., Champion, M. M., Sun, L., Champion, P. A. D., Wojcik, R., & Dovichi, N. J.
Affiliations: University of Washington (US)
University of Notre Dame (US)
ORCID: Li, Yihan
Champion, Matthew M.
Sun, Liangliang
Champion, Patricia A. DiGiuseppe
Wojcik, Roza
Venue: Analytical Chemistry
Publisher: American Chemical Society (ACS)
Published: 2012-01-09
Volume: 84
Issue: 3
Pages: 1617-1622
ISSN: 0003-2700 (ISSN-L)
1520-6882
DOI: 10.1021/ac202899p
PMC: PMC3277681
OpenAlex: W2412786668
Cited by: 128
References: 37
Citations by year: 2025: 5 · 2024: 1 · 2022: 8 · 2021: 4 · 2020: 7 · 2019: 7 · 2018: 9 · 2017: 8 · 2016: 12 · 2015: 17 · 2014: 15 · 2013: 23 · 2012: 12
FWCI: 7.25
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Analytical Chemistry (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of General Medical Sciences (R01GM096767)
National Institute of Neurological Disorders and Stroke (R01NS061767)
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, secretome, Mycobacterium marinum, tryptic digest, peptide identification, protein identification, proteomics platforms
MeSH terms: Chromatography, High Pressure Liquid, Peptides, Proteins, Electrophoresis, Capillary, Mycobacterium marinum, Spectrometry, Mass, Electrospray Ionization, Proteomics, Tandem Mass Spectrometry, Chromatography, Reverse-Phase

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Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry as an Alternative Proteomics Platform to Ultraperformance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry for Samples of Intermediate Complexity

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