Thilo Muth

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows Mass spectrometry (MS)-based proteomics is a well-established strategy for analyzing complex biological mixtures. Many MS instruments and data acquisition strategies are available, and the data they a...

We are happy to share that the preprint for Proteobench is available now on biorxiv!
Check it out here: www.biorxiv.org/content/10.6...
Congratulations and thanks to everyone involved for the great effort!

Accurate de novo sequencing of the modified proteome with OmniNovo Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modified proteome. Standar...

Preprint: Accurate de novo sequencing of the modified proteome with OmniNovo
arxiv.org/abs/2512.12272

Antibody-based signal amplification for single-cell proteomics by mass spectrometry Single-cell proteomics by mass spectrometry (scp-MS) detects thousands of proteins per cell, yet low-abundant proteins routinely detected by antibody-based methods are challenging to quantify in the s...

New preprint! 🚀
We introduce AbTags – antibody–peptide fusion proteins that massively amplify signal, enable absolute quantification of binding events, and are read out together with the single-cell proteome by LC–MS.

AbTag platform is patent-pending.
Preprint: www.biorxiv.org/content/10.6...

Evaluation of statistical approaches for differential metaproteomics Metaproteomics characterizes and compares molecular phenotypes of organisms in communities by comprehensively analyzing their protein expression profiles using statistical methods. However, not all st...

Super excited to have this paper out. We developed a complex set of ground truth samples to test more than 110 statistical approaches for differential #metaproteomics
We can now give clear guidance on what tests perform well. Thank you Tjorven Hinzke and
@benoitkunath.bsky.social for the leadership

Meta-PepView: a metaproteomics performance evaluation and visualization platform Microbial community proteomics is rapidly gaining traction as it allows exploration of functional processes in microbial ecosystems. Consequently, there is a growing need for user-friendly tools that ...

Meta-PepView: a metaproteomics performance evaluation and visualization platform
www.biorxiv.org/content/10.6...

Reflection Pretraining Enables Token-Level Self-Correction in Biological Sequence Models Chain-of-Thought (CoT) prompting has significantly advanced task-solving capabilities in natural language processing with large language models. Unlike standard prompting, CoT encourages the model to ...

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 Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...

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...

The solution is right above us. Solar panels on existing buildings, car parks, and along highways generate clean power without sacrificing farmland or wild spaces. Let's use our built world first. #Renewables #Innovation

HDSE-MS: Tandem Mass Spectrum Prediction for Small Molecules via Hierarchical Distance Structural Encoding Tandem mass spectrometry (MS/MS) is a core technology for small molecule structural elucidation in nontargeted metabolomics. However, the limited coverage of experimental spectral libraries presents a major challenge to MS-based small molecule identification. Although spectrum prediction methods offer a promising alternative, existing approaches often suffer from limitations in combinatorial enumeration strategies or insufficient molecular representation capabilities, leading to poor generalizability. To address this, we propose HDSE-MS, an MS/MS spectrum prediction model that integrates a message passing neural network (MPNN) with a Transformer architecture enhanced by hierarchical distance structural encoding (HDSE). By applying graph coarsening, the model transforms molecular graphs into multilevel cluster structures and encodes the hierarchical distances between clusters as structural biases in the Transformer. This enables the joint modeling of molecular substructures, their hierarchical relationships, and long-range dependencies, thereby improving the model’s ability to represent complex molecular structures. We conducted a comprehensive evaluation of HDSE-MS on three benchmark data sets: NIST23, MoNA, and MassBank. Experimental results show that HDSE-MS outperforms existing methods, achieving mean spectral entropy similarities of 0.759, 0.567, and 0.483 under the [M + H]+ ionization mode, respectively. Furthermore, on the external CASMI2022 test set, HDSE-MS achieved a Rank of 220.8 and a Top-1 accuracy of 0.098, demonstrating its strong predictive accuracy, robust generalization, and scalability. The source code is publicly available at https://github.com/lzjforyou/HDSE-MS, and an interactive web service is accessible at https://huggingface.co/spaces/liuzhijin/hdse-ms-attn-viz.

HDSE-MS: Tandem Mass Spectrum Prediction for Small Molecules via Hierarchical Distance Structural Encoding | Analytical Chemistry pubs.acs.org/doi/10.1021/...

New microprotein can help cancer cells overcome stress In a new study published in the journal Nucleic Acid Research, a research team at Karolinska Institutet has performed a large-scale genetic screen to uncover the hidden roles of tiny proteins, so-call...

Researchers have performed a large-scale genetic screen to uncover the hidden roles of #microproteins. One of the discovered microproteins, named PIPPI, was found to protect cells from stress in the endoplasmic reticulum. Published in @narjournal.bsky.social 🧪 #proteomics news.ki.se/new-micropro...

Update and new implementation of the MIRAGE reporting guidelines for mass spectrometry experiments in glycoscience The MIRAGE (Minimum Information Required for A Glycomics Experiment) guidelines for mass spectrometry (MS) data were initially developed to standardize the reporting of instrumentation, data acquisiti...

Cannot hide my joy, relief, excitement being able to share the outcome of persevering (to say the least) collaborative work. So... the MS glyco(proteomics) guidelines are published!! www.mcponline.org/article/S153...
Many thanks to @beilstein-institut.bsky.social @glycosmos.bsky.social @sib.swiss

Proteins plucked from the pages of Renaissance recipes Analyses of German medical manuals from 1531 reveal what ingredients those who handled the books used

It’s the first time that proteomics has been used to analyze Renaissance recipes. The project demonstrates an innovative way to study medicine and the circulation and use of medical recipes from the past. cen.acs.org/analytical-c... #chemsky 🧪

This project started 5 years ago. It led us to add isotope-labeling support to #FragPipe/#IonQuant. Since then, the tools have grown so much and are now widely used in #Chemoproteomics.

Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social

The ProteomeXchange consortium in 2026: making proteomics data FAIR Abstract. The ProteomeXchange consortium of proteomics resources (http://www.proteomexchange.org) was established to standardize open data practices in the

ProteomeXchange consortium in 2026: making proteomics data FAIR url: academic.oup.com/nar/article/...

What Rosalind Franklin truly contributed to the discovery of DNA’s structure Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.

On the event of James Watson's death, I highly recommend this 2023 commentary from @matthewcobb.bsky.social and Nathaniel Comfort with crucial new insights into the discovery of the double helix. (And also check out Cobb's brand new biography of Francis Crick) www.nature.com/articles/d41...

Screenshot of a Tweet pointing out that academic spam is actually in its own way kind of encouraging.

I think about this post every day 🧪

The reaction to this is fascinating. It's like a microcosm of all discussions around AI: lots of enthusiasm, lots of loathing (much of it reflexive), and some wise 'let's maybe try it and see' responses.

Finally, the R package we needed, but don't deserve. I can already hear @benneely.com cackling from across the country.

Thanks to @willfondrie.com for alerting me to this amazing repo.

This is figure 1, which shows abundance, transcription and distribution of hydrogenase genes and H2-related metabolic genes throughout the human gut.

A previously uncharacterized microbial enzyme is responsible for the production of molecular hydrogen in the gut, which drives the growth of other bacteria and has implications for human health, according to a paper in Nature Microbiology. go.nature.com/4oKOveG #microbiome #medsky 🧪

Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flavi...

🧬 Thrilled to share our latest paper in @natmicrobiol.nature.com 📄

A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think.

Our at-scale AI structure prediction gave a complementary perspective on viral evolution.

www.nature.com/articles/s41...

This is figure 1, which shows the summary results from a survey of 306 scientists on data reuse.

In a Consensus Statement in Nature Microbiology, a consortium of #microbiome scientists discusses current sequencing data sharing policies and proposes the use of a Data Reuse Information tag to promote equitable and collaborative data sharing. go.nature.com/4o1Gl1f 🧪

iDeepLC: chemical structure information yields improved retention time prediction of peptides with unseen modifications Deep learning has notably advanced the field of liquid chromatography–mass spectrometry-based proteomics. Accurate prediction of peptide retention times significantly enhances our ability to match LC-...

Our latest paper introduces new methods for improving peptide retention time predictions in proteomics, incorporating chemical structure information to better handle unseen modifications.

Read all about it in our preprint by👉 doi.org/10.1101/2025...

#Proteomics #AI #MachineLearning

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...

Carafe - spectral library prediction for DIA proteomics
www.nature.com/articles/s41...

Challenges and opportunities in mRNA vaccine development against bacteria - Nature Microbiology This Review reflects on the major challenges in bacterial mRNA vaccine design, provides strategies for tailoring mRNA construct design to promote humoral or cellular immunity, and provides an overview...

If you are interested in mRNA vaccines against bacteria, take a look at our recent review. It was a pleasure to write this together with all co-authors! rdcu.be/eyjBq
www.nature.com/articles/s41...

Sure, I know! I lived in Wedding for a while. 😉

Would have been fun to realize that we are actually at the same spot-the same time… 😆

Less is more: academic publishing needs ‘radical change,’ Cambridge press report concludes Academic publishing needs “renewed focus and collective action” to embrace new approaches and ensure the future of the industry, concludes a report from Cambridge University Press, released last we…

“We fundamentally believe that publishing less – but better – is essential for the health of the entire research system worldwide,” the authors of the report state.

I was there, the same day!!! Just checked the meta data of my photo. The almost only difference, it was dark… 😉

From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics pubs.acs.org/doi/10....

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#proteomics #prot-paper