High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore
(2025)
Immunoproteomics : methods and protocols.
In Methods in molecular biology (MIMB)
2980.
p.115-155
- Author
- David Gomez-Zepeda, Julian Beyrle, Annica Preikschat, Arthur Declercq (UGent) , Yannic Chen, Ralf Gabriels (UGent) , Lennart Martens (UGent) , Ute Distler and Stefan Tenzer
- Organization
- Abstract
- Major histocompatibility complex (MHC, or human leukocyte antigen, HLA) peptide ligands can be exploited to develop immunotherapies targeting immunogenic disease-specific immunopeptides, such as virus- or cancer mutation-derived peptides. Liquid chromatography coupled with mass spectrometry (LC-MS)-based immunopeptidomics is the gold standard for identifying MHC ligands. We previously optimized a workflow enabling the identification of more than 10,000 MHC class I ligands per cell line. This process comprises three major steps: (I) a high-recovery immunopeptidome enrichment, (II) an optimized MS acquisition in the timsTOF Pro called Thunder-Data-Dependent Acquisition with Parallel Accumulation-SErial Fragmentation (Thunder-DDA-PASEF), and (III) peptide identification using PEAKS XPro boosted by MS2Rescore data-driven rescoring. Here, we describe our workflow for deep-coverage immunopeptidomics step-by-step, from sample preparation to data analysis and validation.
- Keywords
- immunopeptidomics, human leucocyte antigen, major histocompatibility complex, sample preparation, immunoprecipitation, mass spectrometry, rescoring
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01KAGDKRKTV1N0FWDFCNNX9M6P
- MLA
- Gomez-Zepeda, David, et al. “High-Coverage Immunopeptidomics Using TimsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS2Rescore.” Immunoproteomics : Methods and Protocols, edited by Kelly M. Fulton and Susan M. Twine, 3rd ed., vol. 2980, Humana, 2025, pp. 115–55, doi:10.1007/978-1-0716-4832-2_5.
- APA
- Gomez-Zepeda, D., Beyrle, J., Preikschat, A., Declercq, A., Chen, Y., Gabriels, R., … Tenzer, S. (2025). High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore. In K. M. Fulton & S. M. Twine (Eds.), Immunoproteomics : methods and protocols (3rd ed., Vol. 2980, pp. 115–155). https://doi.org/10.1007/978-1-0716-4832-2_5
- Chicago author-date
- Gomez-Zepeda, David, Julian Beyrle, Annica Preikschat, Arthur Declercq, Yannic Chen, Ralf Gabriels, Lennart Martens, Ute Distler, and Stefan Tenzer. 2025. “High-Coverage Immunopeptidomics Using TimsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS2Rescore.” In Immunoproteomics : Methods and Protocols, edited by Kelly M. Fulton and Susan M. Twine, 3rd ed., 2980:115–55. New York: Humana. https://doi.org/10.1007/978-1-0716-4832-2_5.
- Chicago author-date (all authors)
- Gomez-Zepeda, David, Julian Beyrle, Annica Preikschat, Arthur Declercq, Yannic Chen, Ralf Gabriels, Lennart Martens, Ute Distler, and Stefan Tenzer. 2025. “High-Coverage Immunopeptidomics Using TimsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS2Rescore.” In Immunoproteomics : Methods and Protocols, ed by. Kelly M. Fulton and Susan M. Twine, 2980:115–155. 3rd ed. New York: Humana. doi:10.1007/978-1-0716-4832-2_5.
- Vancouver
- 1.Gomez-Zepeda D, Beyrle J, Preikschat A, Declercq A, Chen Y, Gabriels R, et al. High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore. In: Fulton KM, Twine SM, editors. Immunoproteomics : methods and protocols. 3rd ed. New York: Humana; 2025. p. 115–55.
- IEEE
- [1]D. Gomez-Zepeda et al., “High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore,” in Immunoproteomics : methods and protocols, 3rd ed., vol. 2980, K. M. Fulton and S. M. Twine, Eds. New York: Humana, 2025, pp. 115–155.
@incollection{01KAGDKRKTV1N0FWDFCNNX9M6P,
abstract = {{Major histocompatibility complex (MHC, or human leukocyte antigen, HLA) peptide ligands can be exploited to develop immunotherapies targeting immunogenic disease-specific immunopeptides, such as virus- or cancer mutation-derived peptides. Liquid chromatography coupled with mass spectrometry (LC-MS)-based immunopeptidomics is the gold standard for identifying MHC ligands. We previously optimized a workflow enabling the identification of more than 10,000 MHC class I ligands per cell line. This process comprises three major steps: (I) a high-recovery immunopeptidome enrichment, (II) an optimized MS acquisition in the timsTOF Pro called Thunder-Data-Dependent Acquisition with Parallel Accumulation-SErial Fragmentation (Thunder-DDA-PASEF), and (III) peptide identification using PEAKS XPro boosted by MS2Rescore data-driven rescoring. Here, we describe our workflow for deep-coverage immunopeptidomics step-by-step, from sample preparation to data analysis and validation.}},
author = {{Gomez-Zepeda, David and Beyrle, Julian and Preikschat, Annica and Declercq, Arthur and Chen, Yannic and Gabriels, Ralf and Martens, Lennart and Distler, Ute and Tenzer, Stefan}},
booktitle = {{Immunoproteomics : methods and protocols}},
editor = {{Fulton, Kelly M. and Twine, Susan M.}},
isbn = {{9781071648315}},
issn = {{1064-3745}},
keywords = {{immunopeptidomics,human leucocyte antigen,major histocompatibility complex,sample preparation,immunoprecipitation,mass spectrometry,rescoring}},
language = {{eng}},
pages = {{115--155}},
publisher = {{Humana}},
series = {{Methods in molecular biology (MIMB)}},
title = {{High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore}},
url = {{http://doi.org/10.1007/978-1-0716-4832-2_5}},
volume = {{2980}},
year = {{2025}},
}
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