Research Explorer

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Researcher

Ralf Gabriels

Publications & Research Data

Awards & Distinctions

50 Results

2026

iDeepLC : chemical structure information yields improved retention time prediction of peptides with unseen modifications

Alireza NameniArthur DeclercqRalf GabrielsRobbe DevreeseSven DegroeveAmélie De MaesschalckMaarten DhaenensCristina ChivaEduard SabidóLennart Martens et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

Large-scale proteomics profiling of peripheral blood of DM1 patients identifies biomarkers for disease severity and functional capacity

Daniël van AsTine ClaeysRenee SalzDelphi Van HaverSara DufourAmber van DeelenJolein GloerichRalf GabrielsPieter Jan VoldersVera Dobelmann et al.

A1 Journal Article in JOURNAL OF NEUROMUSCULAR DISEASES

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

Caroline JachmannZhi SunKevin VelgheFlorence Arsène-PloetzeAurélie HirschlerJasper ZuallaertChristine CarapitoRobbin BouwmeesterKay NieseltEric W. Deutsch et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

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

Koina : democratizing machine learning for proteomics research

Ludwig LautenbacherKevin L. YangTobias KockmannChristian PanseWassim GabrielDulguun BoldElias KahlMatthew ChambersBrendan X. MacLeanKai Li et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

MzPeak : designing a scalable, interoperable, and future-ready mass spectrometry data format

Tim Van Den BosscheTheodore AlexandrovAivett BilbaoWout BittremieuxFederico Ivan BriganteMatthew Chase ChambersJoshua CharkowEric DeutschAndrew W. DowseyYasin El Abiead et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

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

An StaesTeresa MaiaSara DufourRobbin BouwmeesterRalf GabrielsLennart MartensKris GevaertFrancis ImpensSimon Devos

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Bioinformatics pipeline for processing single-cell data

Arthur DeclercqNina DemeulemeesterRalf GabrielsRobbin BouwmeesterSven DegroeveLennart Martens

Bookchapter in Mass spectrometry based single cell 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

Proceedings of the EuBIC-MS developers meeting 2023

Pedro BeltraoTim Van Den BosscheRalf GabrielsTanja HolsteinTobias KockmannAlireza NameniChristian PanseRalph SchlapbachLudwig LautenbacherMatthias Mattanovich et al.

A1 Journal Article in JOURNAL OF PROTEOMICS

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

Joshua KleinHenry LamTytus D. MakWout BittremieuxYasset Perez-RiverolRalf GabrielsJim ShofstahlHelge HechtPierre-Alain BinzShin Kawano et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

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

Large-scale proteomics profiling of peripheral blood of DM1 patients identifies biomarkers for disease severity and physical activity

P. 't HoenD. van AsTine ClaeysR. SalzRalf GabrielsFrancis ImpensPieter-Jan VoldersLennart MartensB. van Engelen

Proteomics standards initiative at twenty years : current activities and future work

Eric W. DeutschJuan Antonio VizcaínoAndrew R. JonesPierre-Alain BinzHenry LamJoshua KleinWout BittremieuxYasset Perez-RiverolDavid L. TabbMathias Walzer et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics

Tobias G. RehfeldtRalf GabrielsRobbin BouwmeesterSiegfried GessulatBenjamin A. NeelyMagnus PalmbladYasset Perez-RiverolTobias SchmidtJuan Antonio VizcaínoEric W. Deutsch

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions

Myrsini SakarikaFrederiek-Maarten KerckhofLotte Van PeteghemAlexandra Pinto Martins PereiraTim Van Den BosscheRobbin BouwmeesterRalf GabrielsDelphi Van HaverBarbara UlčarLennart Martens et al.

A1 Journal Article in MICROBIAL CELL FACTORIES

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

A comprehensive evaluation of consensus spectrum generation methods in proteomics

Xiyang LuoWout BittremieuxJohannes GrissEric W. DeutschTimo SachsenbergLev I. LevitskyMark V. IvanovJulia A. BubisRalf GabrielsHenry Webel et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

Bart Van PuyveldeSimon DaledSander WillemsRalf GabrielsAnne Gonzalez de PeredoKarima ChaouiEmmanuelle Mouton-BarbosaDavid BouyssiéKurt BoonenChristopher J. Hughes et al.

A1 Journal Article in SCIENTIFIC DATA

Cov²MS : an automated and quantitative matrix-independent assay for mass spectrometric measurement of SARS-CoV-2 nucleocapsid protein

Bart Van PuyveldeKatleen Van UytfangheLaurence Van OudenhoveRalf GabrielsTessa Van RoyenArne MatthysMorteza RazaviRichard YipTerry PearsonNicolas Drouin et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes

Rupert MayerRein VerbekeCaroline AsselmanIlke AernoutAdillah GulDenzel EggermontKatie BoucherFabien Henri TheryTeresa MaiaHans Demol et al.

A1 Journal Article in NATURE COMMUNICATIONS

Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

Sven DegroeveRalf GabrielsKevin VelgheRobbin BouwmeesterNatalia TichshenkoLennart Martens

Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Ralf GabrielsLennart MartensSven Degroeve

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms

Richard D. LeDucEric W. DeutschPierre-Alain BinzRyan T. FellersAnthony J. CesnikJoshua A. KleinTim Van Den BosscheRalf GabrielsArshika YalavarthiYasset Perez-Riverol et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

ProteomicsML : an online platform for community-curated datasets and tutorials for machine learning in proteomics

Tobias RehfeldtRalf GabrielsRobbin BouwmeesterSiegfried GessulatBenjamin NeelyMagnus PalmbladYasset Perez-RiverolTobias SchmidtJuan Antonio VizcaínoEric Deutsch

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

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay ShiferawRalf GabrielsRobbin BouwmeesterTim Van Den BosscheElien VandermarliereLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2021

Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatLaurence Van OudenhoveRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid Verhelst et al.

A2 Journal Article in JACS AU

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Robbin BouwmeesterRalf GabrielsNiels HulstaertLennart MartensSven Degroeve

A1 Journal Article in NATURE METHODS

Ion mobility coupled to a time-of-flight mass analyzer combined with fragment intensity predictions improves identification of classical bioactive peptides and small open reading frame-encoded peptides

Marlies PeetersGeert BaggermanRalf GabrielsElise PepermansGerben MenschaertKurt Boonen

A1 Journal Article in FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY

MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Ralf GabrielsRobbin BouwmeesterJasper ZuallaertLennart MartensSven Degroeve

Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection

Renee SalzRobbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan VoldersPeter A.C. ’t Hoen

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Spectral prediction features as a solution for the search space size problem in proteogenomics

Steven VerbruggenSiegfried GessulatRalf GabrielsAnna MatsarokiHendrik Van de VoordeBernhard KusterSven DegroeveLennart MartensWim Van CriekingeMathias Wilhelm et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Universal Spectrum Identifier for mass spectra

Eric W. DeutschYasset Perez-RiverolJeremy CarverShin KawanoLuis MendozaTim Van Den BosscheRalf GabrielsPierre-Alain BinzBenjamin PullmanZhi Sun et al.

A1 Journal Article in NATURE METHODS

2020

COSS : a fast and user-friendly tool for spectral library searching

Genet Abay ShiferawElien VandermarliereNiels HulstaertRalf GabrielsLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Christopher AshwoodWout BittremieuxEric W. DeutschNadezhda T. DonchevaViktoria DorferRalf GabrielsVladimir GorshkovSurya GuptaAndrew R. JonesLukas Käll et al.

A2 Journal Article in EUPA OPEN PROTEOMICS

Removing the hidden data dependency of DIA with predicted spectral libraries

Bart Van PuyveldeSander WillemsRalf GabrielsSimon DaledLaura De ClerckSofie Vande CasteeleAn StaesFrancis ImpensDieter DeforceLennart Martens et al.

A1 Journal Article in PROTEOMICS

The age of data-driven proteomics : how machine learning enables novel workflows

Robbin BouwmeesterRalf GabrielsTim Van Den BosscheLennart MartensSven Degroeve

A1 Journal Article in PROTEOMICS

The HUPO-PSI standardized spectral library format

Ralf GabrielsNuno BandeiraWout BittremieuxJeremy J CarverMatthew ChambersShin KawanoHenry LamTytus MakYasset Perez-RiverolBenjamin J Pullman et al.

2019

Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

A1 Journal Article in NUCLEIC ACIDS RESEARCH