Ghent University Academic Bibliography

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- Book Chapter
High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore

David Gomez-Zepeda, Julian Beyrle, Annica Preikschat, Arthur Declercq (UGent) , Yannic Chen, Ralf Gabriels (UGent) , Lennart Martens (UGent) , Ute Distler and Stefan Tenzer

(2025) Immunoproteomics : methods and protocols. In Methods in molecular biology (MIMB) 2980. p.115-155
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- Journal Article
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TIMS2Rescore : a data dependent acquisition-parallel accumulation and serial fragmentation-optimized data-driven rescoring pipeline based on MS2Rescore

Arthur Declercq (UGent) , Robbe Devreese (UGent) , Jonas Scheid, Caroline Jachmann (UGent) , Tim Van Den Bossche (UGent) , Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurelie Hirschler, Jonathan R. Krieger, et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(3). p.1067-1076
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Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model

David Gomez-Zepeda, Danielle Arnold-Schild, Julian Beyrle, Arthur Declercq (UGent) , Ralf Gabriels (UGent) , Elena Kumm, Annica Preikschat, Mateusz Krzysztof Łącki, Aurélie Hirschler, Jeewan Babu Rijal, et al.

(2024) NATURE COMMUNICATIONS. 15.
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- Journal Article
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- open access
Ionmob : a Python package for prediction of peptide collisional cross-section values

David Teschner, David Gomez-Zepeda, Arthur Declercq (UGent) , Mateusz K Łącki, Seymen Avci, Konstantin Bob, Ute Distler, Thomas Michna, Lennart Martens (UGent) , Stefan Tenzer, et al.

(2023) BIOINFORMATICS. 39(9).
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pH-degradable, bisphosphonate-loaded nanogels attenuate liver fibrosis by repolarization of M2-type macrophages

Leonard Kaps, Anne Huppertsberg, Niklas Choteschovsky, Adrian Klefenz, Feyza Durak, Babara Schrörs, Mustafa Diken, Emma Eichler, Sebastian Rosigkeit, Sascha Schmitt, et al.

(2022) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 119(12).
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- Miscellaneous
Proteomics Standards Initiative : fifteen years of progress and future work

Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert (UGent) , et al.

(2017) JOURNAL OF PROTEOME RESEARCH. 16(12). p.4288-4298

Academic Bibliography

High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore

TIMS2Rescore : a data dependent acquisition-parallel accumulation and serial fragmentation-optimized data-driven rescoring pipeline based on MS2Rescore

Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model

Ionmob : a Python package for prediction of peptide collisional cross-section values

pH-degradable, bisphosphonate-loaded nanogels attenuate liver fibrosis by repolarization of M2-type macrophages

Proteomics Standards Initiative : fifteen years of progress and future work

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