Ghent University Academic Bibliography

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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Transglutaminase mediated crosslinking of pea protein : from rheology to proteomics

A. Mukherjee, Jasper Van Pee (UGent) , D. Duijsens, T. Grauwet, I. Van de Voorde, I. Fraeye and F. Weiland

(2026) FOOD HYDROCOLLOIDS. 173.

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Journal Article
A1
open access

The microbiologist's guide to metaproteomics

Tim Van Den Bossche (UGent) , Jean Armengaud, Dirk Benndorf, Jose Alfredo Blakeley‐Ruiz, Madita Brauer, Kai Cheng, Marybeth Creskey, Daniel Figeys, Lucia Grenga, Timothy J. Griffin, et al.

(2025) IMETA. 4(3).

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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

Koina : democratizing machine learning for proteomics research

Ludwig Lautenbacher, Kevin L. Yang, Tobias Kockmann, Christian Panse, Wassim Gabriel, Dulguun Bold, Elias Kahl, Matthew Chambers, Brendan X. MacLean, Kai Li, et al.

(2025) NATURE COMMUNICATIONS. 16(1).

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Miscellaneous

Metaproteomics beyond databases : addressing the challenges and potentials of de novo sequencing

Tim Van Den Bossche (UGent) , Denis Beslic, Sam van Puyenbroeck (UGent) , Tomi Suomi, Tanja Holstein (UGent) , Lennart Martens (UGent) , Laura L. Elo and Thilo Muth

(2025) PROTEOMICS. 25(17-18). p.51-61

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Journal Article
A1
open access

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

Arslan Siraj, Robbin Bouwmeester (UGent) , Arthur Declercq (UGent) , Luisa Welp, Aleksandar Chernev, Alexander Wulf, Henning Urlaub, Lennart Martens (UGent) , Sven Degroeve (UGent) , Oliver Kohlbacher, et al.

(2024) PROTEOMICS. 24(8).

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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

The proteomics standards initiative standardized formats for spectral libraries and fragment ion peak annotations : mzSpecLib and mzPAF

Joshua Klein, Henry Lam, Tytus D. Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels (UGent) , Jim Shofstahl, Helge Hecht, Pierre-Alain Binz, Shin Kawano, et al.

(2024) ANALYTICAL CHEMISTRY. 96(46). p.18491-18501

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Journal Article
A1
open access

Quality control for the target decoy approach for peptide identification

Elke Debrie, Milan Malfait, Ralf Gabriels (UGent) , Arthur Declercq (UGent) , Adriaan Sticker, Lennart Martens (UGent) and Lieven Clement (UGent)

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.350-358

Academic Bibliography

Unlocking the next decade of proteomics with standardized, structured metadata

Transglutaminase mediated crosslinking of pea protein : from rheology to proteomics

The microbiologist's guide to metaproteomics

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

Koina : democratizing machine learning for proteomics research

Metaproteomics beyond databases : addressing the challenges and potentials of de novo sequencing

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

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

The proteomics standards initiative standardized formats for spectral libraries and fragment ion peak annotations : mzSpecLib and mzPAF

Quality control for the target decoy approach for peptide identification

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