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Analytical Chemistry|July 8, 2025
Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2DeepRobbe Devreese, Alireza Nameni, Arthur Declercq, et al.Analytical Chemistry|June 8, 2026
iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen ModificationsAlireza Nameni, Arthur Declercq, Ralf Gabriels, et al.Nature Communications|February 10, 2026
Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setupsRobbin Bouwmeester, Alireza Nameni, Arthur Declercq, et al.Journal of Proteome Research|March 13, 2025
Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and RescoringPatrick Willems, Fabien Thery, Laura Van Moortel, et al.Journal of Proteome Research|July 14, 2026
Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring MethodsSander Heyndrickx, Robbin Bouwmeester, Arthur Declercq, et al.Journal of Proteomics|July 11, 2026
Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS membersDirk Winkelhardt, Julia P Schessner, Sven Berres, et al.Journal of Proteome Research|February 7, 2025
TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2RescoreArthur Declercq, Robbe Devreese, Jonas Scheid, et al.Nature Communications|November 11, 2025
Koina: Democratizing machine learning for proteomics researchLudwig Lautenbacher, Kevin L Yang, Tobias Kockmann, et al.Pageof 1