Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis

Krokhin, Oleg V.; Anderson, Geoffrey; Spicer, Vic; Sun, Liangliang; Dovichi, Norman J.

doi:10.1021/acs.analchem.6b04544

Cited by 53Advanced Proteomics Techniques and ApplicationsMicrofluidic and Capillary Electrophoresis ApplicationsMass Spectrometry Techniques and Applications

Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis

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Krokhin, Oleg V., Anderson, Geoffrey, Spicer, Vic, Sun, Liangliang, Dovichi, Norman J.·2017·Analytical Chemistry

DOI 10.1021/acs.analchem.6b04544PMC PMC5651133

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Abstract

A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge ( Z ) and size (molecular mass, M ) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies. The extended size of the data set (>4000 peptides) permits access to many sequence-specific factors that impact peptide mobility. The presence of acidic residues Asp and Glu near the peptide N-terminus is by far the most prominent among them. The induction effect of the side chain of N-terminal Asp reduces the basicity of the N-terminal amino group and, as hence, its charge, by ∼0.27 units, lowering mobility. The correlation of the model ( R 2 ∼ 0.995) indicates that the peptide separation process in CZE is relatively simple and can be predicted to a much higher precision than current RP-HPLC models. Similar to RP-HPLC prediction studies, we anticipate future developments that introduce peptide migration standards, collect larger data sets for modeling through the alignment of multiple CZE-MS acquisitions, and study of the behavior of peptides carrying post-translational modifications. The increased size of data sets will also permit investigation of the fine-scale effects of peptide secondary structure on peptide mobility. We observed that peptides with higher helical propensity tend to have higher than predicted electrophoretic mobility; the incorporation of these features into CZE migration models will require significantly larger data sets.

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The Dovichi group reported a sequence-specific model to predict peptide electrophoretic mobility via CZE separations.
“The Dovichi group reported a sequence-specific model to predict peptide electrophoretic mobility via CZE separations75.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [75]
Acidic residues Asp and Glu next to the N-terminus were observed to most influence the deviation of experimental mobility values from classical model predictions.
“Acidic residues (Asp and Glu) next to the N-terminus were observed to most influence the deviation of experimental mobility values from values predicted via classical models.”
From Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019) · cites this paper as [75]

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Authors: Krokhin, O. V., Anderson, G., Spicer, V., Sun, L., & Dovichi, N. J.
Affiliations: University of Manitoba (CA)
Michigan State University (US)
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
Corresponding author: Krokhin, Oleg V.
ORCID: Krokhin, Oleg V.
Spicer, Vic
Sun, Liangliang
Venue: Analytical Chemistry
Publisher: American Chemical Society (ACS)
Published: 2017-01-19
Volume: 89
Issue: 3
Pages: 2000-2008
ISSN: 0003-2700 (ISSN-L)
1520-6882
DOI: 10.1021/acs.analchem.6b04544
PMC: PMC5651133
OpenAlex: W2569641810
Cited by: 53
References: 53
Citations by year: 2026: 1 · 2025: 1 · 2024: 10 · 2023: 2 · 2022: 5 · 2021: 6 · 2020: 3 · 2019: 8 · 2018: 10 · 2017: 7
FWCI: 3.78
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: Natural Sciences and Engineering Research Council of Canada (RGPIN-2016-05963)
National Institutes of Health (R01GM096767)
Topics: Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Physical Sciences › Engineering › Biomedical Engineering › Microfluidic and Capillary Electrophoresis Applications
Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords: capillary zone electrophoresis, tryptic peptides, peptide charge, peptide size, shotgun proteomics, peptide secondary structure, helical propensity
MeSH terms: Aspartic Acid, Chromatography, High Pressure Liquid, HeLa Cells, Humans, Models, Chemical, Peptides, Mass Spectrometry, Trypsin, Glutamic Acid, Electrophoresis, Capillary, Electrophoretic Mobility Shift Assay, Chromatography, Reverse-Phase, High-Throughput Screening Assays

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Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis

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