Patrick Willems

The paper compares DIA and DDA methods for immunopeptidomics, showing DIA improves detection of low-abundant bacterial epitopes from Listeria monocytogenes.

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

Scywalker provides a scalable analysis pipeline for nanopore single-cell transcriptome data, showing good correlation with short-read analyses and enabling isoform-level cell-type-specific expression identification.

CysQuant quantifies cysteine oxidation and protein abundance using DDA or DIA-MS, revealing redox changes in Arabidopsis exposed to light.

The paper uses AlphaFold2 predicted structures to analyze cysteine disulfides and metal binding sites in plant proteomes, finding high agreement with experimental structures and evolutionary trends in metal binding.

The paper introduces the Plant PTM Viewer, a database integrating over 200,000 PTM sites across five plant species to explore protein modifications and their functional implications.