Robbe Devreese

Predicting and Elucidating Peptide Retention Mechanisms with Graph Attention Networks

The paper introduces a deep learning model to predict peptide retention times in liquid chromatography and identifies key factors influencing retention through saliency mapping.

LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

iDeepLC: chemical structure information yields improved retention time prediction of peptides with unseen modifications

iDeepLC improves retention time prediction for peptides with unseen modifications by incorporating chemical structural information, outperforming previous models.

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

The paper improves IM2Deep to predict collisional cross-sections for peptides with multiple conformations, using a comprehensive dataset and tailored architecture.

DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setups

DeepLC uses transfer learning to improve LC retention time prediction across different experimental setups and peptide modifications.

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

The paper improves bacterial epitope discovery by integrating multiple search engines and rescoring, increasing peptide identification by 27% and detecting 18 new bacterial peptides.

TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore

TIMS2Rescore is a data-driven rescoring pipeline optimized for DDA-PASEF data that improves protein identification in proteomics analyses.