MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates. Declercq et al. Molecular and Cellular Proteomics, 2022. DOI: 10.1016/j.mcpro.2022.100266.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Van Den Bossche et al. Nature Communications, 2021. DOI: 10.1038/s41467-021-27542-8.

DeepLC can predict retention times for peptides that carry as-yet unseen modifications. Bouwmeester et al. Nature Methods, 2021. DOI: 10.1038/s41592-021-01301-5.

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. Gabriels et al. Nucleic Acids Research, 2019. DOI: 10.1093/nar/gkz299.

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions. Silva et al. Bioinformatics, 2019. DOI: 10.1093/bioinformatics/btz383.