| DeepLC can predict retention times for peptides that carry as-yet unseen modifications R Bouwmeester, R Gabriels, N Hulstaert, L Martens, S Degroeve Nature Methods 18 (11), 1363-1369, 2021 | 197 | 2021 |
| Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques R Gabriels, L Martens, S Degroeve Nucleic Acids Research, 2019 | 108 | 2019 |
| MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates A Declercq, R Bouwmeester, A Hirschler, C Carapito, S Degroeve, ... Molecular & Cellular Proteomics 21 (8), 100266, 2022 | 77 | 2022 |
| Universal Spectrum Identifier for mass spectra EW Deutsch, Y Perez-Riverol, J Carver, S Kawano, L Mendoza, ... Nature Methods 18 (7), 768-770, 2021 | 71 | 2021 |
| Removing the hidden data dependency of DIA with predicted spectral libraries B Van Puyvelde, S Willems, R Gabriels, S Daled, L De Clerck, ... Proteomics 20 (3-4), 1900306, 2020 | 60 | 2020 |
| The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel Workflows R Bouwmeester, R Gabriels, T Van Den Bossche, L Martens, S Degroeve Proteomics 20 (21-22), 1900351, 2020 | 54 | 2020 |
| Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes RL Mayer, R Verbeke, C Asselman, I Aernout, A Gul, D Eggermont, ... Nature Communications 13 (1), 6075, 2022 | 47 | 2022 |
| Cov-MS: a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients B Van Puyvelde, K Van Uytfanghe, O Tytgat, L Van Oudenhove, ... Jacs Au 1 (6), 750-765, 2021 | 41 | 2021 |
| Spectral prediction features as a solution for the search space size problem in proteogenomics S Verbruggen, S Gessulat, R Gabriels, A Matsaroki, H Van de Voorde, ... Molecular & Cellular Proteomics 20, 100076, 2021 | 41 | 2021 |
| A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics B Van Puyvelde, S Daled, S Willems, R Gabriels, AG de Peredo, ... Scientific Data 9 (1), 2022 | 35 | 2022 |
| Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work EW Deutsch, JA Vizcaíno, AR Jones, PA Binz, H Lam, J Klein, ... Journal of Proteome Research, 2023 | 31 | 2023 |
| ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification S Degroeve, R Gabriels, K Velghe, R Bouwmeester, N Tichshenko, ... BioRxiv, 2021.07. 02.450686, 2021 | 29 | 2021 |
| COSS: A fast and user-friendly tool for spectral library searching GA Shiferaw, E Vandermarliere, N Hulstaert, R Gabriels, L Martens, ... Journal of proteome research 19 (7), 2786-2793, 2020 | 23 | 2020 |
| Proteomics Standards Initiative’s ProForma 2.0: Unifying the encoding of proteoforms and peptidoforms RD LeDuc, EW Deutsch, PA Binz, RT Fellers, AJ Cesnik, JA Klein, ... Journal of proteome research 21 (4), 1189-1195, 2022 | 21 | 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 |
| Personalized proteome: Comparing proteogenomics and open variant search approaches for single amino acid variant detection R Salz, R Bouwmeester, R Gabriels, S Degroeve, L Martens, PJ Volders, ... Journal of Proteome Research 20 (6), 3353-3364, 2021 | 18 | 2021 |
| 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 |
| ProteomicsML: an online platform for community-curated data sets and tutorials for machine learning in proteomics TG Rehfeldt, R Gabriels, R Bouwmeester, S Gessulat, BA Neely, ... Journal of proteome research 22 (2), 632-636, 2023 | 14 | 2023 |
| Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined with Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open … MKR Peeters, G Baggerman, R Gabriels, E Pepermans, G Menschaert, ... Frontiers in Cell and Developmental Biology 9, 2562, 2021 | 14 | 2021 |
Lennart MartensSenior Full Professor of Systems Biology, Ghent University and VIB, Ghent, BelgiumVerified email at UGent.be