VIB-UGent Center for Medical Biotechnology

MoDPA: Inferring Modification-dependent Protein Associations from Uniformly Reprocessed Mass Spectrometry

Post-translational modifications (PTMs) are key regulators of protein function and cellular processes; however, the overall principles of PTM co-regulation and crosstalk remain to be fully understood. Here, we present Modification-Dependent Protein Associations (MoDPA), a framewo...

Proximity biotinylation at the host-Shigella interface reveals UFMylation as an antibacterial pathway

Abstract Host cells contest invasion by intracellular bacterial pathogens with multiple strategies that recognise and/or damage the bacterial surface. To identify host defence factors targeted to intracellular bacteria, we developed a proximity biotinylation approach coupled to q...

Machine learning-based rescoring with MS²Rescore boosts peptide identification and taxonomic specificity in metaproteomics

Abstract Background Metaproteomics, the study of the collective proteome within microbial ecosystems, has gained increasing interest over the past decade. However, peptide identification rates in metaproteomics remain low compared to single-species proteomics. A key challenge is...

Optimizing efficacy to safety ratio of glucocorticoids in rheumatoid arthritis models by leveraging PPARα agonism

ABSTRACT Objectives Glucocorticoids remain essential therapies for several immune- and inflammatory diseases such as rheumatoid arthritis (RA) but are notorious for their (metabolic) side effects. Given the anti-inflammatory and metabolically favorable actions of peroxisome-proli...

From gatekeepers to regenerators: the plasticity of Paneth cells

Paneth cells (PCs) are secretory cells in the small intestine with functions in intestinal homeostasis and innate immunity, with recent studies showing their ability to dedifferentiate and contribute to epithelial regeneration after injury. In this issue of The EMBO Journal, Yang...