Ghent University Academic Bibliography

Journal Article
A1
open access

A multiyear longitudinal harmonization study of quality controls in mass spectrometry proteomics core facilities

Cristina Chiva, Roger Olivella, An Staes (UGent) , Teresa Maia (UGent) , Christian Panse, Karel Stejskal, Thibaut Douché, Bérangère Lombard, Andrea Schuhmann, Damarys Loew, et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(2). p.397-409

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Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

Tibo Vande Moortele (UGent) , Bram Devlaminck, Simon Van de Vyver (UGent) , Tim Van Den Bossche (UGent) , Lennart Martens (UGent) , Peter Dawyndt (UGent) , Bart Mesuere (UGent) and Pieter Verschaffelt (UGent)

(2025) JOURNAL OF PROTEOME RESEARCH. 24(2). p.949-954

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Journal Article
A1
open access

PTMVision : an interactive visualization webserver for post-translational modifications of proteins

Simon Hackl, Caroline Jachmann (UGent) , Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens (UGent) and Kay Nieselt

(2025) JOURNAL OF PROTEOME RESEARCH. 24(2). p.919-928

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Journal Article
A1
open access

Exploring the tomato root protein network exploited by core type 3 effectors from the Ralstonia solanacearum species complex

Joren De Ryck, Veronique Jonckheere (UGent) , Brigitte De Paepe, Annick De Keyser (UGent) , Nemo Peeters, Johan Van Vaerenbergh, Jane Debode (UGent) , Petra Van Damme (UGent) and Sofie Goormachtig (UGent)

(2025) JOURNAL OF PROTEOME RESEARCH. 24(2). p.696-709

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Journal Article
A1
open access

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

Patrick Willems (UGent) , Fabien Henri Thery (UGent) , Laura Van Moortel (UGent) , Margaux De Meyer (UGent) , An Staes (UGent) , Adillah Gul (UGent) , Lyudmila Kovalchuke (UGent) , Arthur Declercq (UGent) , Robbe Devreese (UGent) , Robbin Bouwmeester (UGent) , et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(4). p.2141-2151

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Journal Article
A1
open access

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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Benefit of in silico predicted spectral libraries in data-independent acquisition data analysis workflows

An Staes (UGent) , Teresa Maia (UGent) , Sara Dufour (UGent) , Robbin Bouwmeester (UGent) , Ralf Gabriels (UGent) , Lennart Martens (UGent) , Kris Gevaert (UGent) , Francis Impens (UGent) and Simon Devos (UGent)

(2024) JOURNAL OF PROTEOME RESEARCH. 23(6). p.2078-2089

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Journal Article
A1
open access

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Louise M. Buur, Arthur Declercq (UGent) , Marina Strobl, Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) , Lennart Martens (UGent) , Viktoria Dorfer and Ralf Gabriels (UGent)

(2024) JOURNAL OF PROTEOME RESEARCH. 23(8). p.3200-3207

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Journal Article
A1
open access

Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins

Tine Claeys (UGent) , Maxime Menu, Robbin Bouwmeester (UGent) , Kris Gevaert (UGent) and Lennart Martens (UGent)

(2023) JOURNAL OF PROTEOME RESEARCH. 22(4). p.1181-1192

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Journal Article
A1
open access

Toward an integrated machine learning model of a proteomics experiment

Benjamin A. Neely, Viktoria Dorfer, Lennart Martens (UGent) , Isabell Bludau, Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) , Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, et al.

(2023) JOURNAL OF PROTEOME RESEARCH. 22(3). p.681-696

Academic Bibliography

A multiyear longitudinal harmonization study of quality controls in mass spectrometry proteomics core facilities

Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

PTMVision : an interactive visualization webserver for post-translational modifications of proteins

Exploring the tomato root protein network exploited by core type 3 effectors from the Ralstonia solanacearum species complex

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

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

Benefit of in silico predicted spectral libraries in data-independent acquisition data analysis workflows

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins

Toward an integrated machine learning model of a proteomics experiment

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