Publications

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes
Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and …
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MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented peptides on almost all cells that can be used in …
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MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
A comprehensive evaluation of consensus spectrum generation methods in proteomics
Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of …
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Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide …
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A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction …
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Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide …
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MS²DIP: Highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Accurate MS2 spectrum predictions enable drastic improvements in peptide identification workflows. This identification improvement is …
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
The inclusion of peptide retention time prediction promises to remove peptide identification ambiguity in complex liquid …
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
timsTOF analysis combined with fragment intensity predictions results in improved identification of classical bioactive peptides and sORF-encoded peptides
Bioactive peptides exhibit key roles in a wide variety of complex processes, such as regulation of body weight, learning, aging, and …
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Universal Spectrum Identifier for mass spectra
Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is …
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Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
Discovery of variant peptides such as a single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized …
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Spectral prediction features as a solution for the search space size problem in proteogenomics
Proteogenomics approaches often struggle with the distinction between true and false peptide-to-spectrum matches as the database size …
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Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, …
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, Laura De Clerck, Laura Corveleyn, Sander Willems, Nathan Debunne, Evelien Wynendaele, Bart De Spiegeleer, Peter Judak, Kris Roels, Laurie De Wilde, Peter Van Eenoo, Tim Reyns, Marc Cherlet, Emmie Dumont, Griet Debyser, Ruben t’Kindt, Koen Sandra, Surya Gupta, Nicolas Drouin, Amy Harms, Thomas Hankemeier, Donald JL Jones, Pankaj Gupta, Dan Lane, Catherine S Lane, Said El Ouadi, Jean-Baptiste Vincendet, Nick Morrice, Stuart Oehrle, Nikunj Tanna, Steve Silvester, Sally Hannam, Florian C Sigloch, Andrea Bhangu-Uhlmann, Jan Claereboudt, N Leigh Anderson, Morteza Razavi, Sven Degroeve, Lize Cuypers, Christophe Stove, Katrien Lagrou, Geert A Martens, Dieter Deforce, Lennart Martens, Johannes PC Vissers, Maarten Dhaenens
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Proceedings of the EuBIC-MS 2020 Developers’ Meeting
The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13th to January …
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The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows
A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include …
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The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows
Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
Abstract Data-independent acquisition (DIA) generates comprehensive yet complex mass spectrometric data, which imposes the use of …
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Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
The HUPO-PSI standardized spectral library format
More and more proteomics datasets are becoming available in public repositories. The knowledge embedded in these datasets can be used …
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MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

An important step in high-throughput mass spectrometry-based proteomics is the correct identification of peptide MS² fragmentation …
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Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide’s fragmentation mass spectrum. Since …
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Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques

In mass spectrometry-based proteomics, sequence database search engines have proven to be the gold standard in peptide spectrum …
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