Personal profile
Scientific Career
Mathias Wilhelm studied bioinformatics (B.Sc.) and informatics in the natural sciences (M.Sc.) at the University Bielefeld. After an employment at the Harvard Medical School in the Children’s Hospital Boston in the group of Dr. Hanno Steen, he started his PhD in computational proteomics at the TUM. His dissertation was on "An in-memory platform for the exploration and analysis of big data in biology" - now known as ProteomicsDB. In 2017, he became the bioinformatics group leader at the Chair of Proteomics and Bioanalytics. In 2021, Mathias Wilhelm was appointed to the professorship for Computational Mass Spectrometry at TUM. He is a co-founder of the biotech companies OmicScouts GmbH and MSAID GmbH, both opperating in the field of proteomics.
Education/Academic qualification
Group leader bioinformatics, Chair of Bioanalytics
Jun 2017 → Feb 2021
PhD, An in-memory platform for the exploration and analysis of big data in biology, Chair of Bioanalytics
Aug 2012 → May 2017
Research assistant, Boston Children's Hospital
Feb 2012 → Jul 2012
Master, Informatics in the Natural Sciences, Universität Bielefeld
Oct 2009 → Oct 2011
Bachelor, Bioinformatics and Genome Research, Universität Bielefeld
Oct 2006 → Oct 2009
External positions
Core member, Technical University of Munich
2024 → …
Co-founder and Sharehold, MSAID GmbH
1 Aug 2019 → …
Co-founder and Sharehold, OmicScouts GmbH
1 Jun 2014 → …
Keywords
- QA75 Electronic computers. Computer science
- Bioinformatics
- Proteomics
- Machine Learning
- Database
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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SDG 3 Good Health and Well-being -
SDG 9 Industry, Innovation, and Infrastructure
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Collaborations and top research areas from the last five years
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Reducing Non-Human Primates in Non-Clinical Safety Assessment: The European Initiative on Minipig and Micropig Models
Flisikowska, T. (PI), Norton, T. (PI), Mair, K. H. (PI), Van Cruchten, S. (PI), Wilhelm, M. (PI), Dines, A. (PI) & Wolf, E. (Spokesperson)
1/10/24 → 30/09/29
Project: Research
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NHPig: Reducing Non-Human Primates in Non-Clinical Safety Assessment: The European Initiative on Minipig and Micropig Models
Ebner, F. (CoPI), Wilhelm, M. (CoPI), Flisikowska, T. (CoPI), Norton, T. (CoPI), Mair, K. H. (CoPI), Van Cruchten, S. (CoPI), Dines, A. (CoPI), Wolf, E. (Spokesperson) & Summerfield, A. (CoPI)
1/10/24 → 30/09/29
Project: Research
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LRTN360: The Proteomes that Feed the World - 360° leadership research-training network, Part Phytopathology
Küster, B. (PI), Poppenberger, B. (PI), Schwechheimer, C. (CoPI), Frischmann, D. (CoPI), Wilhelm, M. (CoPI), Gutjahr, C. (CoPI), Heinzlmeir, S. (CoPI), Schön, C.-C. (CoPI), Ludwig, C. (CoPI), Pauling, J. K. (CoPI), Hückelhoven, R. (CoPI) & Dawid, C. (CoPI)
1/10/22 → 30/09/26
Project: Research
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DROP2AI: Drug Response Prediction using Proteomics and AI
Wilhelm, M. (PI), Rad, R. (PI), List, M. (PI), Küster, B. (PI) & Saur, D. (PI)
1/03/23 → 28/02/26
Project: Research
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Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset
Rajczewski, A. T., Mehta, S., Wagner, R., Gabriel, W., Johnson, J., Do, K., Vintila, S., Wilhelm, M., Kleiner, M., Searle, B. C., Griffin, T. J. & Jagtap, P. D., 6 Jan 2026, In: Journal of Proteomics. 322, 105549.Research output: Contribution to journal › Article › peer-review
Open Access -
High-throughput chemical proteomics workflow for profiling protein citrullination dynamics
Meelker González, R., Laposchan, S., Riedel, E., Fürst, A., O’Sullivan, N., Gabriel, W., Wilhelm, M., Knolle, P. A., Médard, G., Kuster, B. & Lee, C. Y., Dec 2026, In: Nature Communications. 17, 1, 1982.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage
Levin, N., Saylan, C. C., Lapin, J., Demyanenko, Y., Yang, K. L., Sidda, J., Nesvizhskii, A. I., Wilhelm, M. & Mohammed, S., 23 Mar 2026, In: Nature Methods.Research output: Contribution to journal › Article › peer-review
Open Access -
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Picciani, M., Soleymaniniya, A., Müller, J., Sakhteman, A., Tzanakis, K., Bernett, J., Kahl, E., Hamood, F., Kersting, J., Pourjam, M., Nagai, L. A. E., List, M., Kuster, B., The, M. & Wilhelm, M., 6 Jan 2026, In: Nucleic Acids Research. 54, 1, p. D470-D480Research output: Contribution to journal › Article › peer-review
Open Access -
Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides
Klaproth-Andrade, D., Bruns, Y., Gabriel, W., Nix, C., Bergant, V., Pichlmair, A., Wilhelm, M. & Gagneur, J., Feb 2026, In: Molecular and Cellular Proteomics. 25, 2, p. 1-18 18 p., 101501.Research output: Contribution to journal › Article › peer-review
Open Access