prof. dr. Sven Degroeve

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

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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Book Chapter

Bioinformatics pipeline for processing single-cell data

Arthur Declercq (UGent) , Nina Demeulemeester, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) and Lennart Martens (UGent)

(2024) Mass spectrometry based single cell proteomics. In Methods in molecular biology (MIMB) 2817. p.221-239

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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

Updated MS²PIP web server supports cutting-edge proteomics applications

Arthur Declercq (UGent) , Robbin Bouwmeester (UGent) , Cristina Chiva, Eduard Sabido, Aurelie Hirschler, Christine Carapito, Lennart Martens (UGent) , Sven Degroeve (UGent) and Ralf Gabriels (UGent)

(2023) NUCLEIC ACIDS RESEARCH. 51(W1). p.W338-W342

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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

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Miscellaneous
open access

PhosphoLingo : protein language models for phosphorylation site prediction

Jasper Zuallaert (UGent) , Pathmanaban Ramasamy (UGent) , Robbin Bouwmeester (UGent) , Nico Callewaert (UGent) and Sven Degroeve (UGent)

(2023) BioRXiv.

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Journal Article
A1
open access

psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results

Ralf Gabriels (UGent) , Arthur Declercq (UGent) , Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) and Lennart Martens (UGent)

(2022) JOURNAL OF PROTEOME RESEARCH. 22(2). p.557-560

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Miscellaneous
open access

Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results

Ralf Gabriels (UGent) , Arthur Declercq (UGent) , Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) and Lennart Martens (UGent)

(2022) ChemRxiv.

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Journal Article
A1
open access

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur Declercq (UGent) , Robbin Bouwmeester (UGent) , Aurélie Hirschler, Christine Carapito, Sven Degroeve (UGent) , Lennart Martens (UGent) and Ralf Gabriels (UGent)

(2022) MOLECULAR & CELLULAR PROTEOMICS. 21(8).

Academic Bibliography

prof. dr. Sven Degroeve

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

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

Bioinformatics pipeline for processing single-cell data

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

Updated MS²PIP web server supports cutting-edge proteomics applications

Toward an integrated machine learning model of a proteomics experiment

PhosphoLingo : protein language models for phosphorylation site prediction

psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results

Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

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