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Researcher
Ralf Gabriels
Profile
Projects
Publications
Activities
Awards & Distinctions
36
Results
2024
Benefit of in silico predicted spectral libraries in data-independent acquisition data analysis workflows
An Staes
Teresa Maia
Sara Dufour
Robbin Bouwmeester
Ralf Gabriels
Lennart Martens
Kris Gevaert
Francis Impens
Simon Devos
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2024
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
Marina Strobl
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
Viktoria Dorfer
Ralf Gabriels
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2024
Proceedings of the EuBIC-MS developers meeting 2023
Pedro Beltrao
Tim Van Den Bossche
Ralf Gabriels
Tanja Holstein
Tobias Kockmann
Alireza Nameni
Christian Panse
Ralph Schlapbach
Ludwig Lautenbacher
Matthias Mattanovich
et al.
A1
Journal Article
in
JOURNAL OF PROTEOMICS
2024
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
David Gomez-Zepeda
Danielle Arnold-Schild
Julian Beyrle
Arthur Declercq
Ralf Gabriels
Elena Kumm
Annica Preikschat
Mateusz Krzysztof Łącki
Aurélie Hirschler
Jeewan Babu Rijal
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2024
2023
Proteomics standards initiative at twenty years : current activities and future work
Eric W. Deutsch
Juan Antonio Vizcaíno
Andrew R. Jones
Pierre-Alain Binz
Henry Lam
Joshua Klein
Wout Bittremieux
Yasset Perez-Riverol
David L. Tabb
Mathias Walzer
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics
Tobias G. Rehfeldt
Ralf Gabriels
Robbin Bouwmeester
Siegfried Gessulat
Benjamin A. Neely
Magnus Palmblad
Yasset Perez-Riverol
Tobias Schmidt
Juan Antonio Vizcaíno
Eric W. Deutsch
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
Quality control for the target decoy approach for peptide identification
Elke Debrie
Milan Malfait
Ralf Gabriels
Arthur Declercq
Adriaan Sticker
Lennart Martens
Lieven Clement
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions
Myrsini Sakarika
Frederiek-Maarten Kerckhof
Lotte Van Peteghem
Alexandra Pinto Martins Pereira
Tim Van Den Bossche
Robbin Bouwmeester
Ralf Gabriels
Delphi Van Haver
Barbara Ulčar
Lennart Martens
et al.
A1
Journal Article
in
MICROBIAL CELL FACTORIES
2023
Updated MS²PIP web server supports cutting-edge proteomics applications
Arthur Declercq
Robbin Bouwmeester
Cristina Chiva
Eduard Sabido
Aurelie Hirschler
Christine Carapito
Lennart Martens
Sven Degroeve
Ralf Gabriels
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2023
2022
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
Bart Van Puyvelde
Simon Daled
Sander Willems
Ralf Gabriels
Anne Gonzalez de Peredo
Karima Chaoui
Emmanuelle Mouton-Barbosa
David Bouyssié
Kurt Boonen
Christopher J. Hughes
et al.
A1
Journal Article
in
SCIENTIFIC DATA
2022
A comprehensive evaluation of consensus spectrum generation methods in proteomics
Xiyang Luo
Wout Bittremieux
Johannes Griss
Eric W. Deutsch
Timo Sachsenberg
Lev I. Levitsky
Mark V. Ivanov
Julia A. Bubis
Ralf Gabriels
Henry Webel
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
Cov²MS : an automated and quantitative matrix-independent assay for mass spectrometric measurement of SARS-CoV-2 nucleocapsid protein
Bart Van Puyvelde
Katleen Van Uytfanghe
Laurence Van Oudenhove
Ralf Gabriels
Tessa Van Royen
Arne Matthys
Morteza Razavi
Richard Yip
Terry Pearson
Nicolas Drouin
et al.
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2022
Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes
Rupert Mayer
Rein Verbeke
Caroline Asselman
Ilke Aernout
Adillah Gul
Denzel Eggermont
Katie Boucher
Fabien Henri Thery
Teresa Maia
Hans Demol
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2022
Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification
Sven Degroeve
Ralf Gabriels
Kevin Velghe
Robbin Bouwmeester
Natalia Tichshenko
Lennart Martens
Preprint
2022
MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates
Arthur Declercq
Robbin Bouwmeester
Aurélie Hirschler
Christine Carapito
Sven Degroeve
Lennart Martens
Ralf Gabriels
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2022
Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods
Ralf Gabriels
Lennart Martens
Sven Degroeve
Dissertation
2022
Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms
Richard D. LeDuc
Eric W. Deutsch
Pierre-Alain Binz
Ryan T. Fellers
Anthony J. Cesnik
Joshua A. Klein
Tim Van Den Bossche
Ralf Gabriels
Arshika Yalavarthi
Yasset Perez-Riverol
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
ProteomicsML : an online platform for community-curated datasets and tutorials for machine learning in proteomics
Tobias Rehfeldt
Ralf Gabriels
Robbin Bouwmeester
Siegfried Gessulat
Benjamin Neely
Magnus Palmblad
Yasset Perez-Riverol
Tobias Schmidt
Juan Antonio Vizcaíno
Eric Deutsch
Preprint
2022
Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results
Ralf Gabriels
Arthur Declercq
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
Preprint
2022
Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator
Genet Abay Shiferaw
Ralf Gabriels
Robbin Bouwmeester
Tim Van Den Bossche
Elien Vandermarliere
Lennart Martens
Pieter-Jan Volders
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results
Ralf Gabriels
Arthur Declercq
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
2021
Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients
Bart Van Puyvelde
Katleen Van Uytfanghe
Olivier Tytgat
Laurence Van Oudenhove
Ralf Gabriels
Robbin Bouwmeester
Simon Daled
Tim Van Den Bossche
Pathmanaban Ramasamy
Sigrid Verhelst
et al.
A2
Journal Article
in
JACS AU
2021
DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Robbin Bouwmeester
Ralf Gabriels
Niels Hulstaert
Lennart Martens
Sven Degroeve
A1
Journal Article
in
NATURE METHODS
2021
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 Peeters
Geert Baggerman
Ralf Gabriels
Elise Pepermans
Gerben Menschaert
Kurt Boonen
A1
Journal Article
in
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
2021
MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates
Ralf Gabriels
Robbin Bouwmeester
Jasper Zuallaert
Lennart Martens
Sven Degroeve
C3
Conference
2021
Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection
Renee Salz
Robbin Bouwmeester
Ralf Gabriels
Sven Degroeve
Lennart Martens
Pieter-Jan Volders
Peter A.C. ’t Hoen
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2021
Spectral prediction features as a solution for the search space size problem in proteogenomics
Steven Verbruggen
Siegfried Gessulat
Ralf Gabriels
Anna Matsaroki
Hendrik Van de Voorde
Bernhard Kuster
Sven Degroeve
Lennart Martens
Wim Van Criekinge
Mathias Wilhelm
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2021
Universal Spectrum Identifier for mass spectra
Eric W. Deutsch
Yasset Perez-Riverol
Jeremy Carver
Shin Kawano
Luis Mendoza
Tim Van Den Bossche
Ralf Gabriels
Pierre-Alain Binz
Benjamin Pullman
Zhi Sun
et al.
A1
Journal Article
in
NATURE METHODS
2021
2020
COSS : a fast and user-friendly tool for spectral library searching
Genet Abay Shiferaw
Elien Vandermarliere
Niels Hulstaert
Ralf Gabriels
Lennart Martens
Pieter-Jan Volders
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2020
Proceedings of the EuBIC-MS 2020 Developers’ Meeting
Christopher Ashwood
Wout Bittremieux
Eric W. Deutsch
Nadezhda T. Doncheva
Viktoria Dorfer
Ralf Gabriels
Vladimir Gorshkov
Surya Gupta
Andrew R. Jones
Lukas Käll
et al.
A2
Journal Article
in
EUPA OPEN PROTEOMICS
2020
Removing the hidden data dependency of DIA with predicted spectral libraries
Bart Van Puyvelde
Sander Willems
Ralf Gabriels
Simon Daled
Laura De Clerck
Sofie Vande Casteele
An Staes
Francis Impens
Dieter Deforce
Lennart Martens
et al.
A1
Journal Article
in
PROTEOMICS
2020
The HUPO-PSI standardized spectral library format
Ralf Gabriels
Nuno Bandeira
Wout Bittremieux
Jeremy J Carver
Matthew Chambers
Shin Kawano
Henry Lam
Tytus Mak
Yasset Perez-Riverol
Benjamin J Pullman
et al.
C3
Conference
2020
The age of data-driven proteomics : how machine learning enables novel workflows
Robbin Bouwmeester
Ralf Gabriels
Tim Van Den Bossche
Lennart Martens
Sven Degroeve
A1
Journal Article
in
PROTEOMICS
2020
2019
Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques
Ralf Gabriels
Lennart Martens
Sven Degroeve
C3
Conference
2019
MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Ralf Gabriels
Lennart Martens
Sven Degroeve
C3
Conference
2019
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Ralf Gabriels
Lennart Martens
Sven Degroeve
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2019