Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring DOI Creative Commons
Patrick J. Willems, Fabien Théry, Laura Van Moortel

и другие.

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted antigens that can serve as vaccine candidates. However, reliable identification epitopes is challenged their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident immunopeptides. Immunopeptidomics data cell cultures with Listeria monocytogenes were searched four different search engines, PEAKS, Comet, Sage and MSFragger, followed data-driven rescoring MS2Rescore. Compared individual engine results, this integrated workflow boosted immunopeptide average 27% led high-confidence detection 18 additional peptides (+27%) matching 15 proteins (+36%). Despite strong agreement between a small number spectra (<1%) had ambiguous matches multiple excluded ensure identifications. Finally, demonstrate our sensitive timsTOF SCP acquisition find rescoring, now inclusion ion mobility features, identifies 76% more compared Q Exactive HF acquisition. Together, results how integration along maximizes identification, boosting for development.

Язык: Английский

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring DOI Creative Commons
Patrick J. Willems, Fabien Théry, Laura Van Moortel

и другие.

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted antigens that can serve as vaccine candidates. However, reliable identification epitopes is challenged their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident immunopeptides. Immunopeptidomics data cell cultures with Listeria monocytogenes were searched four different search engines, PEAKS, Comet, Sage and MSFragger, followed data-driven rescoring MS2Rescore. Compared individual engine results, this integrated workflow boosted immunopeptide average 27% led high-confidence detection 18 additional peptides (+27%) matching 15 proteins (+36%). Despite strong agreement between a small number spectra (<1%) had ambiguous matches multiple excluded ensure identifications. Finally, demonstrate our sensitive timsTOF SCP acquisition find rescoring, now inclusion ion mobility features, identifies 76% more compared Q Exactive HF acquisition. Together, results how integration along maximizes identification, boosting for development.

Язык: Английский

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