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

Overview

Journal Anal Chem

Specialty Chemistry

Date 2011 Dec 21

PMID 22182061

Citations 70

Authors

Yihan Li

Matthew M Champion

Liangliang Sun

Patricia A DiGiuseppe Champion

Roza Wojcik

Norman J Dovichi

Affiliations

Soon will be listed here.

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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