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A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.

Patrick Willems^1,2,3,4, Fabien Thery^1,2, Laura Van Moortel^1,2

¹VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.

Journal of Proteome Research

|March 13, 2025

Summary

This summary is machine-generated.

This study presents an optimized bioinformatics framework to improve the identification of bacterial immunopeptides, crucial for developing new vaccines against infections like Listeria. The integrated approach significantly boosts the detection of bacterial epitopes.

Keywords:

Listeria monocytogenes TIMS2Rescore immunopeptides ion mobility mass spectrometry search engines

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Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Published on: May 23, 2021

Area of Science:

Immunology
Bioinformatics
Vaccine Development

Background:

Mass spectrometry enables discovery of bacterial antigens for vaccines.
Identifying low-abundance bacterial epitopes remains a significant challenge.

Purpose of the Study:

To develop and validate an optimized bioinformatic framework for enhanced identification of bacterial immunopeptides.
To improve the confident detection of bacterial epitopes for vaccine candidate discovery.

Main Methods:

Integrated immunopeptidomics data analysis using four search engines (PEAKS, Comet, Sage, MSFragger).
Data-driven rescoring with MS2Rescore, incorporating ion mobility features.
Validation with timsTOF SCP and Q Exactive HF data acquisition.

Main Results:

The integrated workflow increased bacterial immunopeptide identification by 27% compared to individual search engines.
18 additional bacterial peptides and 15 new Listeria protein matches were identified with high confidence.
Rescoring with ion mobility features identified 76% more peptides on timsTOF SCP compared to Q Exactive HF.

Conclusions:

Integration of multiple search engines and data-driven rescoring maximizes bacterial immunopeptide identification.
This enhanced approach significantly boosts the detection of high-confidence bacterial epitopes for vaccine development.
The optimized framework improves the discovery pipeline for novel vaccine candidates.