| MS2Rescore: data-driven rescoring dramatically boosts immunopeptide identification rates A Declercq, R Bouwmeester, A Hirschler, C Carapito, S Degroeve, ... Molecular & Cellular Proteomics 21 (8), 2022 | 77 | 2022 |
| Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model D Gomez-Zepeda, D Arnold-Schild, J Beyrle, A Declercq, R Gabriels, ... Nature Communications 15 (1), 2288, 2024 | 18 | 2024 |
| MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0 LM Buur, A Declercq, M Strobl, R Bouwmeester, S Degroeve, L Martens, ... Journal of proteome research, 2024 | 17 | 2024 |
| Updated MS²PIP web server supports cutting-edge proteomics applications A Declercq, R Bouwmeester, C Chiva, E Sabidó, A Hirschler, C Carapito, ... Nucleic Acids Research 51 (W1), W338-W342, 2023 | 17 | 2023 |
| Ionmob: a Python package for prediction of peptide collisional cross-section values D Teschner, D Gomez-Zepeda, A Declercq, MK Łącki, S Avci, K Bob, ... Bioinformatics 39 (9), btad486, 2023 | 13 | 2023 |
| psm_utils: A high-level Python API for parsing and handling peptide-spectrum matches and proteomics search results R Gabriels, A Declercq, R Bouwmeester, S Degroeve, L Martens Journal of Proteome Research 22 (2), 557-560, 2022 | 7 | 2022 |
| Thunder-DDA-PASEF enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCov-2 spike protein epitopes D Gomez-Zepeda, D Arnold-Schild, J Beyrle, E Kumm, U Distler, H Schild, ... | 4 | 2023 |
| TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore A Declercq, R Devreese, J Scheid, C Jachmann, TV Den Bossche, ... bioRxiv, 2024.05. 29.596400, 2024 | 3 | 2024 |
| Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links A Siraj, R Bouwmeester, A Declercq, L Welp, A Chernev, A Wulf, H Urlaub, ... Proteomics 24 (8), 2300144, 2024 | 2 | 2024 |
| TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore A Declercq, R Devreese, J Scheid, C Jachmann, T Van Den Bossche, ... Journal of Proteome Research, 2025 | | 2025 |
| High-coverage immunopeptidomics using timsTOF mass spectrometers with Thunder-DDA-PASEF boosted by MS2Rescore D Gomez-Zepeda, J Beyrle, A Preikschat, A Declercq, Y Chen, R Gabriels, ... | | 2024 |
| Bioinformatics Pipeline for Processing Single-Cell Data A Declercq, N Demeulemeester, R Gabriels, R Bouwmeester, S Degroeve, ... Mass Spectrometry Based Single Cell Proteomics, 221-239, 2024 | | 2024 |
| Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring P Willems, F Thery, L Van Moortel, M De Meyer, A Staes, A Gul, ... bioRxiv, 2024.11. 22.624860, 2024 | | 2024 |
| Data-driven methods for improved immunopeptide identification in mass spectrometry A Declercq Ghent University, 2021 | | 2021 |