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Researcher
Robbin Bouwmeester
Profile
Projects
Publications
Activities
Awards & Distinctions
27
Results
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
2023
FAVA : high-quality functional association networks inferred from scRNA-seq and proteomics data
Mikaela Koutrouli
Pau Piera Líndez
Katerina Nastou
Robbin Bouwmeester
Simon Rasmussen
Lennart Martens
Lars Juhl Jensen
Preprint
2023
Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins
Tine Claeys
Maxime Menu
Robbin Bouwmeester
Kris Gevaert
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
PhosphoLingo : protein language models for phosphorylation site prediction
Jasper Zuallaert
Pathmanaban Ramasamy
Robbin Bouwmeester
Nico Callewaert
Sven Degroeve
Preprint
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
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
Toward an integrated machine learning model of a proteomics experiment
Benjamin A. Neely
Viktoria Dorfer
Lennart Martens
Isabell Bludau
Robbin Bouwmeester
Sven Degroeve
Eric W. Deutsch
Siegfried Gessulat
Lukas Kaell
Pawel Palczynski
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
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
How sticky are our proteins? Quantifying hydrophobicity of the human proteome
Juami Hermine Mariama van Gils
Dea Gogishvili
Jan van Eck
Robbin Bouwmeester
Erik van Dijk
Sanne Abeln
A2
Journal Article
in
BIOINFORMATICS ADVANCES
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 on large-scale proteomics data identifies tissue- and cell type-specific proteins
Tine Claeys
Maxime Menu
Robbin Bouwmeester
Kris Gevaert
Lennart Martens
Preprint
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
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
Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit
Morgane Boone
Pathmanaban Ramasamy
Jasper Zuallaert
Robbin Bouwmeester
Berre Van Moer
Davy Maddelein
Demet Turan
Niels Hulstaert
Hannah Eeckhaut
Elien Vandermarliere
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
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
2020
Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
A1
Journal Article
in
ANALYTICAL CHEMISTRY
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
The difference is in the details : predicting the LC-IM-MS behaviour of metabolites and peptides
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
Dissertation
2020
2019
A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry : application to the characterisation of metabolites in rat urine
Leanne C Nye
Jonathan P Williams
Nyasha C Munjoma
Marine PM Letertre
Muireann Coen
Robbin Bouwmeester
Lennart Martens
Jonathan R Swann
Jeremy K Nicholson
Robert S Plumb
et al.
A1
Journal Article
in
JOURNAL OF CHROMATOGRAPHY A
2019
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
Ana Sílvia Ferreira Diamantino Coelho e Silva
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
A1
Journal Article
in
BIOINFORMATICS
2019
Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2019