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I’m a bioinformatics research group leader specializing in proteomics—the big-data science of proteins. My work focuses on developing smarter computational tools to make sense of complex biological data. One of my key contributions has been maintaining and improving Percolator, a machine-learning tool that helps researchers identify proteins more accurately from mass spectrometry data. Recently, my team and I developed software tools like PTMNavigator to explore protein modifications and CurveCurator to analyze drug response patterns. By combining computer science, statistics, and biology, I aim to make proteomics research more reliable and insightful. Ultimately, my goal is to help uncover new biological discoveries that could lead to better disease treatments and a deeper understanding of how life works at the molecular level. In my spare time I enjoy learning new languages, traveling and eating delicious food.
Selected Recent Publications
Julian Müller, Florian P. Bayer, Mathias Wilhelm, Maximilian G. Schuh, Bernhard Kuster, & Matthew The (2025). PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways. Nature Communications, 
Florian P. Bayer, Manuel Gander, Bernhard Kuster, & Matthew The (2023). CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves. Nature Communications, 
Jana Zecha, Florian P. Bayer, Svenja Wiechmann, Julia Woortman, Nicola Berner, Julian Müller, … , Matthew The, Mathias Wilhelm, & Bernhard Kuster (2023). Decrypting drug actions and protein modifications by dose-and time-resolved proteomics. Science, 
Open source projects
- PTMNavigator – Discover how PTMs are regulated across biochemical pathways –
- Oktoberfest – Rescore peptide IDs and generate spectral libraries using Prosit –
- CurveCurator – Intuitive dose-response analysis for drug studies –
- Picked Group FDR – Scalable FDR control for protein groups –
- SIMSI-Transfer – Transfers peptide IDs across datasets for higher sensitivity –
- Quandenser – Pre-clusters data for sensitive label-free quantification –
- Triqler – Bayesian analysis for robust protein quantification –
- MaRaCluster – Clusters spectra to improve protein identification –
- Percolator – Machine learning rescoring for better peptide IDs –
- LiveLCA – Real-time tracking for dynamic life cycle assessments –
Experience
2019 – Present
Group Leader Bioinformatics (since 2021) / Postdoctoral Researcher at TU Munich, Chair of Proteomics and Bioanalytics
2014 – 2018
PhD in Biotechnology at KTH – Royal Institute of Technology (SciLifeLab)
Supervisor: Lukas Käll
2011 – 2013
MSc in Scientific computing at TU Berlin / KTH – Royal Institute of Technology
2007 – 2011
BSc in Physics at Leiden University
2007 – 2010
BSc in Applied Mathematics at TU Delft
Address: Chair of Proteomics and Bioanalytics (“Kusterlab”), Emil-Erlenmeyer-Forum 5, 85354 Freising
E-mail: matthew [dot] the [at] tum [dot] de
LinkedIn: http://linkedin.com/in/matthewthe/