Ghent University Academic Bibliography

Journal Article
A1
open access

The Escherichia coli PeptideAtlas build : characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

Caroline Jachmann (UGent) , Zhi Sun, Kevin Velghe (UGent) , Florence Arsène-Ploetze, Aurélie Hirschler, Jasper Zuallaert (UGent) , Christine Carapito, Robbin Bouwmeester (UGent) , Kay Nieselt, Eric W. Deutsch, et al.

(2026) JOURNAL OF PROTEOME RESEARCH. 25(2). p.1027-1041

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Journal Article
A1
open access

Unlocking the next decade of proteomics with standardized, structured metadata

Tim Van Den Bossche (UGent) , Ananth Prakash, Tine Claeys (UGent) , Juan Antonio Vizcaíno and Lennart Martens (UGent)

(2026) JOURNAL OF PROTEOME RESEARCH. 25(2). p.556-561

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Classification of collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline

Ian Engels (UGent) , Alexandra Burnett (UGent) , Prudence Robert (UGent) , Camille Pironneau (UGent) , Grégory Abrams (UGent) , Robbin Bouwmeester (UGent) , Peter Van Der Plaetsen, Kévin Di Modica, Marcel Otte, Lawrence Guy Straus, et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(4). p.1907-1925

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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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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

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 (UGent) , 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

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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Journal Article
A1
open access

Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes

Patrick Willems (UGent) , An Staes (UGent) , Laia Miret Casals (UGent) , Vadim Demichev, Simon Devos (UGent) and Francis Impens (UGent)

(2025) JOURNAL OF PROTEOME RESEARCH. 24(12). p.6295-6304

Academic Bibliography

The Escherichia coli PeptideAtlas build : characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

Unlocking the next decade of proteomics with standardized, structured metadata

Classification of collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline

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

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

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

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

Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes

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