Research Explorer

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Researcher

Arthur Declercq

Publications & Research Data

Awards & Distinctions

17 Results

2026

Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups

Robbin BouwmeesterAlireza NameniArthur DeclercqRobbe DevreeseKevin VelgheVladimir GorshkovPelayo A. PenanesFrank KjeldsenMagali RompaisChristine Carapito et al.

A1 Journal Article in NATURE COMMUNICATIONS

2025

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Robbe DevreeseAlireza NameniArthur DeclercqEmmy TerrynRalf GabrielsFrancis ImpensKris GevaertLennart MartensRobbin Bouwmeester

A1 Journal Article in ANALYTICAL CHEMISTRY

Epitope Odyssey : data-driven tools to extend the known immunopeptide universe

Arthur DeclercqLennart MartensFrancis Impens

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

David Gomez-ZepedaJulian BeyrleAnnica PreikschatArthur DeclercqYannic ChenRalf GabrielsLennart MartensUte DistlerStefan Tenzer

Bookchapter in Immunoproteomics : methods and protocols

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

Patrick WillemsFabien Henri TheryLaura Van MoortelMargaux De MeyerAn StaesAdillah GulLyudmila KovalchukeArthur DeclercqRobbe DevreeseRobbin Bouwmeester et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

MHCquant2 refines immunopeptidomics tumor antigen discovery

Jonas ScheidSteffen LemkeNaomi Hoenisch-GravelAnna DenglerTimo SachsenbergArthur DeclercqRalf GabrielsJens BauerMarcel WackerLeon Bichmann et al.

A1 Journal Article in GENOME BIOLOGY

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

Arthur DeclercqRobbe DevreeseJonas ScheidCaroline JachmannTim Van Den BosscheAnnica PreikschatDavid Gomez-ZepedaJeewan Babu RijalAurelie HirschlerJonathan R. Krieger et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

Bioinformatics pipeline for processing single-cell data

Arthur DeclercqNina DemeulemeesterRalf GabrielsRobbin BouwmeesterSven DegroeveLennart Martens

Bookchapter in Mass spectrometry based single cell proteomics

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

Arslan SirajRobbin BouwmeesterArthur DeclercqLuisa WelpAleksandar ChernevAlexander WulfHenning UrlaubLennart MartensSven DegroeveOliver Kohlbacher et al.

A1 Journal Article in PROTEOMICS

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

Louise M. BuurArthur DeclercqMarina StroblRobbin BouwmeesterSven DegroeveLennart MartensViktoria DorferRalf Gabriels

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

David Gomez-ZepedaDanielle Arnold-SchildJulian BeyrleArthur DeclercqRalf GabrielsElena KummAnnica PreikschatMateusz Krzysztof ŁąckiAurélie HirschlerJeewan Babu Rijal et al.

A1 Journal Article in NATURE COMMUNICATIONS

2023

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

David TeschnerDavid Gomez-ZepedaArthur DeclercqMateusz K ŁąckiSeymen AvciKonstantin BobUte DistlerThomas MichnaLennart MartensStefan Tenzer et al.

A1 Journal Article in BIOINFORMATICS

Quality control for the target decoy approach for peptide identification

Elke DebrieMilan MalfaitRalf GabrielsArthur DeclercqAdriaan StickerLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Updated MS²PIP web server supports cutting-edge proteomics applications

Arthur DeclercqRobbin BouwmeesterCristina ChivaEduard SabidoAurelie HirschlerChristine CarapitoLennart MartensSven DegroeveRalf Gabriels

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2022

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

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

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH