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Updated: Jul 12, 2025
Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
Deep proteome coverage advances knowledge of Treponema pallidum protein expression profiles during infection
Simon Houston1, Alloysius Gomez1, Andrew Geppert1
1Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
Abstract:
Comprehensive proteome-wide analysis of the syphilis spirochete, Treponema pallidum ssp. pallidum, is technically challenging due to high sample complexity, difficulties with obtaining sufficient quantities of bacteria for analysis, and the inherent fragility of the T. pallidum cell envelope which further complicates proteomic identification of rare T. pallidum outer membrane proteins (OMPs). The main aim of the present study was to gain a deeper understanding of the T. pallidum global proteome expression profile under infection conditions. This will corroborate and extend genome annotations, identify protein modifications that are unable to be predicted at the genomic or transcriptomic levels, and provide a foundational knowledge of the T. pallidum protein expression repertoire. Here we describe the optimization of a T. pallidum-specific sample preparation workflow and mass spectrometry-based proteomics pipeline which allowed for the detection of 77% of the T. pallidum protein repertoire under infection conditions. When combined with prior studies, this brings the overall coverage of the T. pallidum proteome to almost 90%. These investigations identified 27 known/predicted OMPs, including potential vaccine candidates, and detected expression of 11 potential OMPs under infection conditions for the first time. The optimized pipeline provides a robust and reproducible workflow for investigating T. pallidum protein expression during infection. Importantly, the combined results provide the deepest coverage of the T. pallidum proteome to date.
Insights
Researchers optimized proteomic analysis for Treponema pallidum (syphilis spirochete), identifying 77% of its proteins during infection. This deep proteome coverage advances understanding of syphilis pathogenesis and potential vaccine targets.
Area of Science:
- Microbiology
- Proteomics
- Infectious Diseases
Background:
- Comprehensive proteome analysis of Treponema pallidum is hindered by sample complexity and bacterial fragility.
- Identifying rare outer membrane proteins (OMPs) in T. pallidum presents significant proteomic challenges.
Purpose of the Study:
- To optimize a sample preparation and mass spectrometry pipeline for T. pallidum proteome analysis.
- To gain a deeper understanding of the T. pallidum global proteome expression profile under infection conditions.
- To identify novel outer membrane proteins (OMPs) and potential vaccine candidates.
Main Methods:
- Development and optimization of a T. pallidum-specific sample preparation workflow.
- Application of a mass spectrometry-based proteomics pipeline for large-scale protein identification.
- Integration of new data with prior proteomic studies for comprehensive coverage.
Main Results:
- Detection of 77% of the T. pallidum protein repertoire under infection conditions.
- Achieved nearly 90% overall proteome coverage when combined with previous studies.
- Identified 27 known/predicted OMPs and detected 11 novel OMPs during infection for the first time.
Conclusions:
- The optimized pipeline offers a robust method for studying T. pallidum protein expression during infection.
- This study provides the deepest proteome coverage of T. pallidum to date.
- Findings enhance genome annotations and identify potential vaccine candidates for syphilis.
