Thilo Muth
Group Leader and Adjunct Professor 🧑🏫 | Public Health | Data Engineering & Visualization | 🧬 Bioinformatics & 📈 Mass Spec Enthusiast | 📍 Berlin | Passionate About Collaboration and Open Science 🔬✨
- Preprint: Accurate de novo sequencing of the modified proteome with OmniNovo arxiv.org/abs/2512.12272
- Preprint: Reflection Pretraining Enables Token-Level Self-Correction in Biological Sequence Models arxiv.org/abs/2512.20954
- Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides - Molecular & Cellular Proteomics www.mcponline.org/article/S153...
- HDSE-MS: Tandem Mass Spectrum Prediction for Small Molecules via Hierarchical Distance Structural Encoding | Analytical Chemistry pubs.acs.org/doi/10.1021/...
- ProteomeXchange consortium in 2026: making proteomics data FAIR url: academic.oup.com/nar/article/...
- Carafe - spectral library prediction for DIA proteomics www.nature.com/articles/s41...
- DicePlot: A package for high dimensional categorical data visualization url: academic.oup.com/bioinformati...
- A Phosphoproteomic Analysis of Mycobacterial PknG-Mediated Host Immune Evasion | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- Published a new article with Roger Karlsson / Uni Gothenburg and Gelio Alves / NIH: From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- Great to see developments for timsTOF data in proteomics and using Rust for it!!! Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- Collaborators published new Review article on #metaproteomics „Contribution of metaproteomics to unveiling the functional role of the gut microbiome in human physiology and metabolism“: doi.org/10.1080/1478...
- Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification - Molecular & Cellular Proteomics www.mcponline.org/article/S153...
- Integrative Omics and AI-Driven Systems Biology: Multilayer Networks Decoding Apis mellifera Health and Resilience | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- Almost missed that. Led by my dear collegue Tim, a great effort using the column storage format Parquet! mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format | Journal of Proteome Research pubs.acs.org/doi/10.1021/... #TeamMassSpec #Proteomics
- 🔬 New tool alert! SequenceAssembler assembles complete proteoform sequences by merging PSM & de novo seq data: - Single-assembly platform with Novor, PEAKS, PatternLab - GUI and one-click install - Tested on BSA & trastuzumab Paper in Journal of Proteomics: www.sciencedirect.com/science/arti...
- ImmunoPepper: Extracting personalized peptides from complex splicing graphs url: academic.oup.com/bioinformati...
- Sounds interesting! This software supports HDX-MS method optimization (structural proteomics), protease characterization, and routine QC in bottom-up #proteomics. DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion | Analytical Chemistry pubs.acs.org/doi/full/10....
- NovoLign: metaproteomics by sequence alignment: academic.oup.com/ismecommun/a...
- New Preprint (AI again…): Representations Augmented Autoregressive Biological Sequence Generation: Application in De Novo Peptide Sequencing. Benchmarked on #antibody data. arxiv.org/abs/2510.08169 #TeamMassSpec #Proteomics
- Metaproteomics Symposium 2026, taking place from June 21–24, 2026, in Dessau-Roßlau, Germany! Join us for talks and discussions with leading experts in the field of metaproteomics. Meet researchers, share your work + explore the advances in metaproteomics research: www.hs-anhalt.de/landingsites...
- 🧠🦠 New study dives beyond taxonomy to explore functional gut microbiome changes in Parkinson’s disease. Using multi-omics, the authors found disrupted microbial gene expression, especially in motility & glutamate pathways, linked to PD and prodromal PD: rdcu.be/eKc1q #microbiome #parkinsons
- After all, spotted a paper that comes without “AI“ as method! The authors present a graph-theory-based framework for 2D MS/MS, enabling <1s/sample de novo sequencing via PageRank-based ion grouping & fragmentation tree reconstruction: pubs.rsc.org/en/content/a... #MassSpec #GraphTheory
- 3001! While I know that citation count doesn‘t necessarily correlate with successful #research, it still is good to know that published studies are being read and eventually have an impact on other researchers… #science #publications
- We have a new preprint out on the potential and limitations of de novo sequencing in MS/MS-based proteomics: www.biorxiv.org/content/10.1...
- PhD Job Alert: PhD position in metaproteome bioinformatics in Ghent/Belgium with a stay at RKI in Berlin. www.ugent.be/en/work/scie... Feel free to share
- Impressive work from great colleagues at RKI. Ultra-fast virus 🦠 diagnostics with mass spec. Original publication on vPro-MS here: www.nature.com/articles/s41...
- New Preprint by MetaProtInit colleagues, with DIA and DDA #metaproteomics data! Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiome doi: doi.org/10.1101/2025...
- Antibodies aren’t genome-encoded, making them hard to analyze with standard proteomics. A new end-to-end workflow enables direct sequencing using AI-driven de novo methods and tailored assembly—advancing precision proteomics. Preprint here: doi.org/10.1101/2025... #proteomics #teammassspec #ai
- Precise Discovery of Novel N-Terminal Proteoforms beyond the Limitations of Proteogenomics and De Novo Sequencing | Analytical Chemistry pubs.acs.org/doi/abs/10.1...
- Homo-Tag-Assembler Assay for Full-Length Antibody Sequencing | Analytical Chemistry pubs.acs.org/doi/abs/10.1...
- New work from great collaboration partners of mine: Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- 🚀 Preprint out by the Noble Lab: Casanovo v5.0 is here! Usability, speed & interoperability all improved — with better-calibrated scores, faster performance, and smoother integration into proteomics workflows. De novo sequencing just got more practical, check it out: dx.doi.org/10.1101/2025...
- UniScore, a unified and universal measure for peptide identification by multiple search engines t.co/oh4mLgHXWc --- #proteomics #prot-preprint t.co/lqDUaJRqua
- To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
- 🎉 2026 marks a double milestone for Metaproteomics: 20 years of #metaproteomics and 10 years since the first MP symposium! Join June 21–24, 2026 in Dessau, Germany for the 7th Metaproteomics Symposium - a unique opportunity to meet, exchange ideas, and explore latest developments: lnkd.in/eBCXTbT9
- Exciting times ahead. Revolutionary study in #Metaproteomics out! Using de novo sequencing and latest LC/MS technology to redefine the „dark metaproteome“: dx.doi.org/10.1038/s414...
- ganon2: up-to-date and scalable metagenomics analysis url: academic.oup.com/nargab/artic...
- Sounds like something for a read in between. New review: Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions academic.oup.com/bib/article/...
- Correct FDR control in proteomics is tricky, and this @natmethods.nature.com study by Wen et. al is a great example highlighting the specific challenges. It provides a formal framework to evaluate entrapment estimation methods. Fantastic read!
Error control in proteomics mass spectrometry analysis is hard. We came up with a way to evaluate error control. Upshot: for old-school DDA data, not so bad. For DIA data, no existing tool successfully controls the false discovery rate! www.nature.com/articles/s41...
- New review article out! Metaproteomics of human microbiota: progress and key challenges for precision medicine Link: www.sciencedirect.com/science/arti... #Metaproteomics #TeamMassSpec #Microbiome
- Foundation Model for MS Proteomics - Preprint out: arxiv.org/abs/2505.10848
- New publication alert. :-) We published our new tool MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics in Journal of Proteome Research pubs.acs.org/doi/10.1021/... #TeamMassSpec #Bioinformatics #Proteomics #Proteogenomics #Pathogens
