Research Explorer

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Researcher

Ralf Gabriels

32 Results

2023

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

2022

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.

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

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.

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

Cov2MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patients

Bart Van PuyveldeKatleen Van UytfangheLaurence Van OudenhoveRalf GabrielsTessa Van RoyenArne MatthysMorteza RazaviRichard YipTerry PearsonMarijn van Hulle et al.

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

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

Ralf GabrielsLennart MartensSven Degroeve

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

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

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

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

Proteomics standards initiatives 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.

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

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

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

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 HUPO-PSI standardized spectral library format

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

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

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