ralf.gabriels.dev
ralf.gabriels.dev
About
Contact
Light
Dark
Automatic
Proteomics
Generating high-quality libraries for DIA datasets
Lecture: Generating high-quality predicted libraries for DIA dataset peptide detection
Ralf Gabriels
Nov 15, 2022
PDF
Slides
DOI
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 …
Rupert L Mayer
,
Rein Verbeke
,
Caroline Asselman
,
Ilke Aernout
,
Adillah Gul
,
Denzel Eggermont
,
Katie Boucher
,
Fabien Thery
,
Teresa M Maia
,
Hans Demol
,
Ralf Gabriels
,
Lennart Martens
,
Christophe Bécavin
,
Stefaan C De Smedt
,
Bart Vandekerckhove
,
Ine Lentacker
,
Francis Impens
DOI
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 …
Arthur Declercq
,
Robbin Bouwmeester
,
Aurélie Degroeve
,
Hirschler
,
Christine Carapito
,
Sven
,
Lennart Martens
,
Ralf Gabriels
PDF
Cite
Code
Project
DOI
Enabling novel and challenging proteomics workflows with MS²Rescore
Talk at the 2022 online EuPA Early-Career Researchers Day on MS²Rescore applications
Ralf Gabriels
Jun 26, 2022
PDF
Slides
DOI
Machine learning to the rescue: Enabling novel proteomics workflows with data-driven bioinformatics methods
Introduction to proteomics, mass spectrometry, and machine learning for a layman audience and a summary of my PhD projects
Ralf Gabriels
May 19, 2022
Slides
DOI
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 …
Xiyang Luo
,
Wout Bittremieux
,
Johannes Griss
,
Eric W. Deutsch
,
Timo Sachsenberg
,
Lev I. Levitsky
,
Mark V. Ivanov
,
Julia A. Bubis
,
Ralf Gabriels
,
Henry Webel
,
Aniel Sanchez
,
Mingze Bai
,
Lukas Käll
,
and Yasset Perez-Riverol*
DOI
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 …
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
,
Lee A. Gethings
,
Yasset Perez-Riverol
,
Nic Bloomfield
,
Stephen Tate
,
Odile Schiltz
,
Lennart Martens
,
Dieter Deforce
,
Maarten Dhaenens
DOI
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 …
Ralf Gabriels
,
Arthur Declercq
,
Robbin Bouwmeester
,
Jasper Zuallaert
,
Lennart Martens
,
Sven Degroeve
PDF
Cite
DOI
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 …
Robbin Bouwmeester
,
Ralf Gabriels
,
Niels Hulstaert
,
Lennart Martens
,
Sven Degroeve
PDF
Cite
Code
Project
DOI
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 …
Marlies KR Peeters
,
Geert Baggerman
,
Ralf Gabriels
,
Elise Pepermans
,
Gerben Menschaert
,
Kurt Boonen
DOI
»
Cite
×