🚨📢 New paper online 🚨📢 Four Xlinking flavors in living cells, up to 1000-fold faster. Highlights include Xlinking kinetics of the RNA-binding proteome and a new way to quantify cytosolic RNA interactions only minutes after ribotoxic stress. #RNASky #Chromatin #Proteomics doi.org/10.1093/nar/...

Rapid photo-crosslinking in living cells reveals protein–nucleic acid dynamics on a timescale of minutes

Abstract. The activation of chemical reactions in living cells using ultraviolet (UV) light enables the interrogation of biomolecules in their native envir

doi.org

New preprint 🚨 We systematically measured 17 million phospho-specific dose-response curves (133 kinase inhibitors × 5 cell lines) to decrypt the kinases that shape the human phosphoproteome. We show that drug perturbation potency (not effect size) links kinases to substrates while controlling FDR.

Florian P Bayer@flobayer.bsky.social · 9mo ago

Did you ever come across a phosphosite in your proteomics data for which nothing was known? - I bet so! We have developed a new strategy termed "potency coherence analysis" that leverages the drug potency dimension in decryptM to decode the kinases that shape the human phosphoproteome. Read more:

Exited to share our latest work! Out now in @natcomms.nature.com Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA! www.nature.com/articles/s41...

Koina: Democratizing machine learning for proteomics research - Nature Communications

Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...

nature.com

Hello Toronto!🍁The Terrific TUM Team is happy to be attending #HUPO2025. Kusterlab, Wilhelmlab and Leelab have a diverse set of presentations for you that we can't wait to share 🤓. We're excited to spend the next days reuniting with old friends and making new connections. See you there!

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...

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

New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...

Peptide-RNA photo-crosslinks with tunable RNA chain map protein-RNA interfaces

Photo-crosslinking mass spectrometry enables the identification of protein-RNA interactions in living cells, pinpointing interaction interfaces at single-amino acid resolution. However, current isolat...

doi.org

New Preprint: High-intensity 365 nm irradiation accelerates photoreactions in living cells by up to 1000×. We show protein–drug 💊, –protein 💪, –DNA 🧬, –RNA 🧬 crosslinking within seconds, and analysis by #massspec for #proteomics, #chembio, #chromatin and #RNAbiology. www.biorxiv.org/content/10.1...

Enhanced photo-crosslinking in living cells with high-intensity longwave ultraviolet light

The activation of chemical reactions in living cells using ultraviolet (UV) light enables the interrogation of biomolecules in their native environment with photoreactive probes or crosslinking reagen...

biorxiv.org

Thanks @tum.de for highlighting Jakob's recent paper in @cellpress.bsky.social in the university news: www.ls.tum.de/en/ls/public... If you haven't had the chance to read the publication, you can check it out here: doi.org/10.1016/j.ce...

Excited to share our latest work published in #ScienceSignaling! 🚀 www.science.org/doi/10.1126/... (1/4)

Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling

Proteomic analyses offer insights into how KRAS inhibitors affect oncogenic KRAS signaling.

science.org

Kusterlab is looking for a new member to join our Bioinformatics team. Apply now if you're interested in working with us!

Another day of #ASMS2025 in Baltimore, and we're back with another poster! Make sure to visit Flo today - he'll present the latest insights from his large-scale decryptM project. Go #TeamMassSpec!

Hello Baltimore! We're looking forward to #ASMS2025 and all the new developments in mass-spec and proteomics. If you're attending today, make sure to check out @msleelab.bsky.social's poster on citrullination in multiple sclerosis. Sophia 'Lapo' Laposchan is excited to see you there!

🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...

The human proteome with direct physical access to DNA

Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes with single-amino-aci...

cell.com

New paper! Our chemoproteomic survey of phenylhydroxamic acids identifies the first drug-like inhibitors for nucleotide-binding protein HINT1 and nucleoside kinases NME1-4. On top, we found probes for the HDAC inhibitor off-target MBLAC2. Check out the open-access article! tinyurl.com/yh92vh6b

Serendipitous and Systematic Chemoproteomic Discovery of MBLAC2, HINT1, and NME1-4 Inhibitors from Histone Deacetylase-Targeting Pharmacophores

Metalloenzyme inhibitors often incorporate a hydroxamic acid moiety to bind the bivalent metal ion cofactor within the enzyme’s active site. Recently, inhibitors of Zn2+-dependent histone deacetylases...

tinyurl.com

Severin Lechner@sevlechner.bsky.social · last yr.

Paper alert! We report the first inhibitors for nucleoside kinases NME1-4 and for the nucleotide-binding protein HINT1. On top, we provide probes for MBLAC2, an off-target of every second (!) hydroxamic acid-based HDAC inhibitor! tinyurl.com/yh92vh6b 👇🧵

New paper! Our chemoproteomic survey of phenylhydroxamic acids identifies the first drug-like inhibitors for nucleotide-binding protein HINT1 and nucleoside kinases NME1-4. On top, we found probes for the HDAC inhibitor off-target MBLAC2. Check out the open-access article! tinyurl.com/yh92vh6b

sev on X: "Paper alert! We report the first inhibitors for nucleoside kinases NME1-4 and for the nucleotide-binding protein HINT1. On top, we provide probes for MBLAC2, an off-target of every second (!) hydroxamic acid-based HDAC inhibitor! https://t.co/uuRCO78xFz 👇🧵" / X

Paper alert! We report the first inhibitors for nucleoside kinases NME1-4 and for the nucleotide-binding protein HINT1. On top, we provide probes for MBLAC2, an off-target of every second (!) hydroxamic acid-based HDAC inhibitor! https://t.co/uuRCO78xFz 👇🧵

x.com

One algorithm to rule them all? CHIMERYS bridges the gap — DDA,DIA and PRM — together at last! With #CHIMERYS, we can now directly compare DDA and DIA data — 🍎 to 🍎 finally made possible. doi.org/10.1038/s41592-025-02663-w #KusterLab #WilhelmLab #MSAID #Proteomics

Unifying the analysis of bottom-up proteomics data with CHIMERYS - Nature Methods

CHIMERYS is a spectrum-centric and data acquisition method-agnostic algorithm for the analysis of MS2 spectra. It is capable of deconvoluting any MS2 spectrum, regardless of whether it was acquired by...

doi.org

3/2025 Issue ➡️ www.embopress.org/toc/17444292... metabolic mutations drive bacterial antibiotic resistance evolution, prior knowledge for GRN inference, HPA drugs fail mood disorder clinical trials Cover: ATR kinase inhibitors work together to overcome chemoresistance @kusterlab.bsky.social

🚀 Exciting news from our lab! Our latest paper has been featured on the cover of @molsystbiol.org - "Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response" by Höfer et al.! 🧬🎉 doi.org/10.1038/s44320-025-00085-6 (1/4)

Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response | Molecular Systems Biology

imageimagePhosphoproteomics unveils the mode of action of clinical ATR inhibitors and explains their synergy with Gemcitabine in pancreatic cancer cells. Viability screening of 146 targeted drugs ide...

doi.org

🎉 We're happy to announce that our latest project was published in @naturecomms.bsky.social this week: PTMNavigator, a #bioinformatics web platform for in-depth analysis of post-translational modification (PTM) perturbation datasets. 📄 doi.org/10.1038/s414... (1/6)

PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways - Nature Communications

Post-translational modifications are important regulators of cellular pathways, but our understanding of these processes is limited. Here, the authors present a web tool that integrates various databa...

doi.org

(1/5) 🚨 New Research Alert! 🚨 Excited to share our latest work in @embojournal.bsky.social "Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study" ✨ doi.org/10.1038/s443... 📌 Key Highlights:

Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study | The EMBO Journal

imageimageFormalin fixed paraffin embedded (FFPE) patient tumor specimens are readily accessible and established gold standard for cancer diagnostics in pathology laboratories. To start building a pan...

doi.org

That's a wrap on #HUPO2024! Kusterlab, Leelab, Wilhelmlab, and BayBioMS had an awesome time in Dresden. It was good to meet so many familiar and new faces in the community. See you next time! https://t.co/n306Mxe1fw

#HUPO2024 starts tomorrow and the Terrific TUM Team is ready! Kusterlab, Wilhelmlab (@wilhelm_compms), Leelab (@msleemslab) and BayBioMS (@BayBioMS) have printed their posters and prepared their talks, and we're very excited for the next days. See you in Dresden! https://t.co/RtEIuAOLok

Shoutout to our colleagues at @proteomicsdb who are working overtime to solve this!

ProteomicsDB has had some downtime lately because of hardware issues. We're sorry for that and promise that it will be up and running again soon! https://t.co/kN4uJ2gMxA

... and it's back: https://t.co/1tFPnJWsyv

Our friends at https://t.co/1tFPnJWsyv are rolling out an update. Stay tuned for new content and features 👀 https://t.co/fpp2LUm3NI

Final Day of #ASMS2024 in Anaheim, but the Terrific TUM Team is far from done! Ludwig from Wilhelmlab will tell you all about Koina today. And at their posters, meet Flo (Kusterlab), Joel (Wilhelmlab), and Miri (@BayBioMS). See you there! One final time: Go #TeamMassSpec! https://t.co/yeX48Go2nZ

Here's to another day of exciting posters and talks at #ASMS2024! Kusterlab and @msleemslab are looking forward to meeting you! https://t.co/ls0R8hhQfu

You're interested in Computational Mass Spec? We got you covered! Check out our three posters today, presenting the latest updates from SIMSI, Prosit, and Oktoberfest! See you at #ASMS2024! 🧪+💻=😍 https://t.co/XJfps6pwWT

What's up Anaheim! The Terrific TUM Team, aka Kusterlab, Wilhelmlab, and Leelab, is excited for #ASMS2024. Here is our program for the next few days. We hope to meet many of you there and are excited to check out all of your presentations! Let's go #TeamMassSpec https://t.co/KoI40riq9A