Thilo Muth
@drmuth.bsky.social
Group Leader and Adjunct Professor 🧑🏫 | Public Health | Data Engineering & Visualization | 🧬 Bioinformatics & 📈 Mass Spec Enthusiast | 📍 Berlin | Passionate About Collaboration and Open Science 🔬✨
Reposted by Thilo Muth
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
Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social
How can we study target engagement and selectivity of covalent inhibitors? Which electrophilic probes are best suited to study a certain amino acid?
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Profiling the proteome-wide selectivity of diverse electrophiles - Nature Chemistry
Covalent inhibitors are powerful entities in drug discovery. Now the amino acid selectivity and reactivity of a diverse electrophile library have been assessed proteome-wide using an unbiased workflow...
www.nature.com
October 30, 2025 at 2:15 PM
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
Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social
ProteomeXchange consortium in 2026: making proteomics data FAIR url: academic.oup.com/nar/article/...
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
academic.oup.com
November 9, 2025 at 7:49 PM
ProteomeXchange consortium in 2026: making proteomics data FAIR url: academic.oup.com/nar/article/...
Reposted by Thilo Muth
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...
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.
www.nature.com
November 7, 2025 at 9:25 PM
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...
Reposted by Thilo Muth
I think about this post every day 🧪
November 7, 2025 at 12:15 PM
I think about this post every day 🧪
Reposted by Thilo Muth
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.
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 7, 2025 at 1:43 PM
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.
Reposted by Thilo Muth
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.
Thanks to @willfondrie.com for alerting me to this amazing repo.
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 7, 2025 at 6:38 PM
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.
Thanks to @willfondrie.com for alerting me to this amazing repo.
Reposted by Thilo Muth
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 🧪
November 5, 2025 at 2:08 PM
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 🧪
Reposted by Thilo Muth
🧬 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...
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...
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...
www.nature.com
November 6, 2025 at 12:52 PM
🧬 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...
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...
Reposted by Thilo Muth
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 🧪
September 30, 2025 at 1:15 PM
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 🧪
Reposted by Thilo Muth
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
Read all about it in our preprint by👉 doi.org/10.1101/2025...
#Proteomics #AI #MachineLearning
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-...
doi.org
November 4, 2025 at 8:53 PM
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
Read all about it in our preprint by👉 doi.org/10.1101/2025...
#Proteomics #AI #MachineLearning
Carafe - spectral library prediction for DIA proteomics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
November 7, 2025 at 7:29 PM
Carafe - spectral library prediction for DIA proteomics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Thilo Muth
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...
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...
www.nature.com
August 1, 2025 at 7:11 PM
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...
www.nature.com/articles/s41...
Reposted by Thilo Muth
“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.
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…
retractionwatch.com
October 21, 2025 at 7:11 PM
“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.
Reposted by Thilo Muth
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....
---
#proteomics #prot-paper
---
#proteomics #prot-paper
October 29, 2025 at 4:20 PM
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....
---
#proteomics #prot-paper
---
#proteomics #prot-paper
Reposted by Thilo Muth
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
Take advantage of this extra time to share your latest proteomics discoveries.
Submit now: www.ushupoconference.org
October 30, 2025 at 8:31 PM
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
Take advantage of this extra time to share your latest proteomics discoveries.
Submit now: www.ushupoconference.org
Reposted by Thilo Muth
Prediction of peptide cleavage sites using protein language models and graph neural networks www.nature.com/artic...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
October 31, 2025 at 10:00 AM
Prediction of peptide cleavage sites using protein language models and graph neural networks www.nature.com/artic...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
Reposted by Thilo Muth
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics - BMC Bioinformatics bmcbioinformatics.bi...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
October 31, 2025 at 1:20 PM
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics - BMC Bioinformatics bmcbioinformatics.bi...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
DicePlot: A package for high dimensional categorical data visualization url: academic.oup.com/bioinformati...
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.
academic.oup.com
November 1, 2025 at 8:22 PM
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/...
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...
pubs.acs.org
November 1, 2025 at 8:15 PM
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/...
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...
pubs.acs.org
November 1, 2025 at 8:14 PM
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/...
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-...
pubs.acs.org
November 1, 2025 at 8:11 PM
Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Reposted by Thilo Muth
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/...
• Especially useful for preclinical metabolites, that have no standards.
Analytical Chemistry (open access article)
pubs.acs.org/doi/10.1021/...
October 30, 2025 at 1:35 PM
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/...
• Especially useful for preclinical metabolites, that have no standards.
Analytical Chemistry (open access article)
pubs.acs.org/doi/10.1021/...
Reposted by Thilo Muth
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...
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...
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. ...
doi.org
October 20, 2025 at 7:07 AM
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...
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...
Reposted by Thilo Muth
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...
www.nature.com/articles/s41...
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods
A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...
www.nature.com
June 16, 2025 at 8:57 PM
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...
www.nature.com/articles/s41...
Reposted by Thilo Muth
Cascadia from @wnoble.bsky.social is a mass spec-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a range of instruments and experimental protocols. www.nature.com/articles/s41...
July 7, 2025 at 10:31 PM
Cascadia from @wnoble.bsky.social is a mass spec-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a range of instruments and experimental protocols. www.nature.com/articles/s41...