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Kusterlab @kusterlab.bsky.social · 29d

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

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Kusterlab @kusterlab.bsky.social · Aug 25

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...

www.biorxiv.org

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Kusterlab @kusterlab.bsky.social · Aug 7

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...

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Kusterlab @kusterlab.bsky.social · Jul 31

If you're a KRAS nerd, get your holistic view of oncogenic KRAS signaling here: www.science.org/doi/10.1126/...
#KRAS #proteomics (4/4)

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

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

www.science.org

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Kusterlab @kusterlab.bsky.social · Jul 31

What makes it even better: All experiments were performed in a dose-resolved manner—so you can dive into dose-response curves in our interactive dashboards! #CurveCurator #BeautifulCurves (3/4)

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Kusterlab @kusterlab.bsky.social · Jul 31

We explore how inhibition of oncogenic KRAS signaling reshapes protein phosphorylation, ubiquitylation, and protein expression—across multiple time points, using various KRAS inhibitors, as well as upstream and downstream pathway inhibitors, in different KRAS-mutant cell lines. (2/4)

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Kusterlab @kusterlab.bsky.social · Jul 31

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.

www.science.org

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Kusterlab @kusterlab.bsky.social · Jul 30

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

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Kusterlab @kusterlab.bsky.social · Jun 4

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!

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Kusterlab @kusterlab.bsky.social · Jun 2

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!

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Kusterlab @kusterlab.bsky.social · May 22

🚨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...

www.cell.com

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Kusterlab @kusterlab.bsky.social · May 9

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

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Kusterlab @kusterlab.bsky.social · May 9

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

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Kusterlab @kusterlab.bsky.social · Apr 22

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

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Reposted by Kusterlab

Molecular Systems Biology @molsystbiol.org · Mar 12

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

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Kusterlab @kusterlab.bsky.social · Mar 4

📢 Read the full paper here: doi.org/10.1038/s44320-025-00085-6 – we’d love to hear your thoughts! #CancerResearch #PDAC #MolecularBiology #Proteomics (4/4)

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

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Kusterlab @kusterlab.bsky.social · Mar 4

🔎 To uncover the molecular mechanisms driving this synergy, we employed both chemo- and phosphoproteomics (decryptM), which revealed how ATR inhibition disrupts the DNA damage response when combined with gemcitabine. (3/4)

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Kusterlab @kusterlab.bsky.social · Mar 4

🧫 Using large-scale phenotypic drug screening, we identified promising drug combinations that enhance tumor cell death - and found Gemcitabine and ATR inhibitors to synergize most effectively. (2/4)

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Kusterlab @kusterlab.bsky.social · Mar 4

🚀 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

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Kusterlab @kusterlab.bsky.social · Feb 4

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