Research Explorer

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Researcher

Ralf Gabriels

23 Results

2022

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

Bart Van PuyveldeSimon DaledRalf GabrielsLennart MartensDieter DeforceMaarten Dhaenens

A comprehensive evaluation of consensus spectrum generation methods in proteomics

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 UytfangheRalf GabrielsTessa Van RoyenArne MatthysXavier SaelensChristophe StoveDieter DeforceLennart MartensMaarten Dhaenens

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterSven 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

2021

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

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid VerhelstLaura De ClerckLaura CorveleynSander WillemsNathan DebunneEvelien WynendaeleBart De SpiegeleerPéter JudákKris RoelsLaurie De WildePeter Van EenooTim ReynsMarc CherletSurya GuptaSven DegroeveChristophe StoveDieter DeforceLennart MartensMaarten Dhaenens

A2 Journal Article in JACS AU

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 PeetersRalf GabrielsGerben Menschaert

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

Robbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms

Tim Van Den BosscheRalf Gabriels

Sensitive and specific spectral library searching with COSS and Percolator

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

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

Steven VerbruggenRalf GabrielsAnna MatsarokiHendrik Van de VoordeSven DegroeveLennart MartensWim Van CriekingeGerben Menschaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Universal Spectrum Identifier for mass spectra

Tim Van Den BosscheRalf Gabriels

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 TytgatRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid VerhelstLaura De ClerckLaura CorveleynNathan DebunneEvelien WynendaeleBart De SpiegeleerPéter JudákKris RoelsLaurie De WildePeter Van EenooTim ReynsMarc CherletSurya GuptaSven DegroeveChristophe StoveDieter DeforceLennart MartensMaarten Dhaenens

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

Robbin BouwmeesterRalf GabrielsNiels HulstaertLennart MartensSven Degroeve

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Ralf GabrielsSurya GuptaBart MesuereTim Van Den BosscheBart Van PuyveldePieter Verschaffelt

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 MartensSven DegroeveMaarten Dhaenens

A1 Journal Article in PROTEOMICS

The HUPO-PSI standardized spectral library format

Ralf GabrielsTim Van Den Bossche

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