Publications of Sander Willems

Skowronek, P.; Wallmann, G.; Wahle, M.; Willems, S.; Mann, M.: An accessible workflow for high-sensitivity proteomics using parallel accumulation–serial fragmentation (PASEF). Nature Protocols (2025)

Strauss, M. T.; Bludau, I.; Zeng, W.-F.; Voytik, E.; Ammar, C.; Schessner, J. P.; Ilango, R.; Gill, M.; Meier, F.; Willems, S. et al.; Mann, M.: AlphaPept: A modern and open framework for MS-based proteomics. Nature Communications 15 (1), 2168 (2024)

Ammar, C.; Schessner, J. P.; Willems, S.; Michaelis, A. C.; Mann, M.: Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes. Molecular & Cellular Proteomics 22 (7), 100581 (2023)

Skowronek, P.; Krohs, F.; Lubeck, M.; Wallmann, G.; Itang, E. C. M.; Koval, P.; Wahle, M.; Thielert, M.; Meier, F.; Willems, S. et al.; Raether, O.; Mann, M.: Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition. Molecular & Cellular Proteomics 22 (2), 100489 (2023)

Zeng, W.-F.; Zhou, X.-X.; Willems, S.; Ammar, C.; Wahle, M.; Bludau, I.; Voytik, E.; Strauss, M. T.; Mann, M.: AlphaPeptDeep: A modular deep learning framework to predict peptide properties for proteomics. Nature Communications 13 (1), 7238 (2022)

Skowronek, P.; Thielert, M.; Voytik, E.; Tanzer, M. C.; Hansen, F. M.; Willems, S.; Karayel, O.; Brunner, A.-D.; Meier, F.; Mann, M.: Rapid and in-depth coverage of the (phospho-) proteome with deep libraries and optimal window design for dia-PASEF. Molecular & Cellular Proteomics 21 (9), 100279 (2022)

Bludau, I.; Willems, S.; Zeng, W.-F.; Strauss, M. T.; Hansen, F. M.; Tanzer, M. C.; Karayel, O.; Schulman, B. A.; Mann, M.: The structural context of posttranslational modifications at a proteome-wide scale. PLoS Biology 20 (5), e3001636 (2022)

Van Puyvelde, B.; Daled, S.; Willems, S.; Gabriels, R.; de Peredo, A. G.; Chaoui, K.; Mouton-Barbosa, E.; Bouyssie, D.; Boonen, K.; Hughes, C. J. et al.; Gethings, L. A.; Perez-Riverol, Y.; Bloomfield, N.; Tate, S.; Schiltz, O.; Martens, L.; Deforce, D.; Dhaenens, M.: A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics. Scientific Data 9 (1), 126 (2022)

Voytik, E.; Bludau, I.; Willems, S.; Hansen, F. M.; Brunner, A.-D.; Strauss, M. T.; Mann, M.: AlphaMap: An open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge. Bioinformatics 38 (3), pp. 849 - 852 (2022)

Verhelst, S.; Van Puyvelde, B.; Willems, S.; Daled, S.; Cornelis, S.; Corveleyn, L.; Willems, E.; Deforce, D.; De Clerck, L.; Dhaenens, M.: A large scale mass spectrometry-based histone screening for assessing epigenetic developmental toxicity. Scientific Reports 12 (1), 1256 (2022)

Daled, S.; Willems, S.; Van Puyvelde, B.; Corveleyn, L.; Verhelst, S.; De Clerck, L.; Deforce, D.; Dhaenens, M.: Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions. Proteomes 9 (2), 17 (2021)