Thilo Muth

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 An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.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

Good news! The #USHUPO2026 abstract submission deadline has been extended through November 19.
Take advantage of this extra time to share your latest proteomics discoveries.
Submit now: www.ushupoconference.org

Prediction of peptide cleavage sites using protein language models and graph neural networks www.nature.com/artic...

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#proteomics #prot-paper

A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics - BMC Bioinformatics bmcbioinformatics.bi...

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#proteomics #prot-paper

DicePlot: A package for high dimensional categorical data visualization AbstractSummary. Visualization of multidimensional, categorical data is a common challenge across scientific domains and, in particular, the life sciences.

DicePlot: A package for high dimensional categorical data visualization url: academic.oup.com/bioinformati...

A Phosphoproteomic Analysis of Mycobacterial PknG-Mediated Host Immune Evasion Pathogenic mycobacteria, such as Mycobacterium tuberculosis, modulate the host immune system to evade clearance and promote long-term persistence, leading to disease progression or latent infection. U...

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 Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

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 Mass spectrometry-based immunopeptidomics is a powerful approach to uncover peptides presented by human leukocyte antigen (HLA) molecules that can guide vaccine design and immunotherapies. While data-...

Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

MRM generation using adaptive modeling of tandem MS data. A simple concept that allows for MRM analysis without the need for standards.
• Especially useful for preclinical metabolites, that have no standards.
Analytical Chemistry (open access article)
pubs.acs.org/doi/10.1021/...

I feel you. Same here… started two groups and raising two kids. Hard but rewarding times! Fully living the life

Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications Protein function is dynamically modulated by post-translational modifications (PTMs). Many different types of PTMs can nowadays be identified and quantified at a large scale using mass spectrometry. ...

Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics!
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...