MS Lee Lab

High-throughput chemical proteomics workflow for profiling protein citrullination dynamics www.nature.com/artic...

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#proteomics #prot-paper

Our proteomics workflow for profiling citrullination dynamics is out 🎉
www.nature.com/articles/s41...
Idea from a journal club discussion + Funding + Determined PhD student + many “this didn’t work…” moments =
A robust, accessible citrullinome enrichment workflow
#proteomics #citrullination #PTM

Hello Toronto! 🇨🇦 The terrific TUM team is on fire today at #HUPO2025!
Don’t miss our postdoc Andreas presenting his peptidome study on 2,000+ plasma samples with unprecedented depth and robustness — catch him at poster session PV.02.065!
#peptidome #proteomics #TUM #HUPO2025 #TTTT

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...

We of course couldn’t let that slip and developed a method:
✅ compatible with tandem MS
✅ strong enrichment efficiency
✅ uses commercial reagents, works in tubes + 96-well plates
We hope it becomes your new favorite for hunting this tiny PTM 🔥
#citrullination #proteomics #ptms

High-throughput chemical proteomics workflow for profiling protein citrullination dynamics Citrullination is a post-translational modification implicated in autoimmune and inflammatory diseases, yet its low abundance and lack of effective enrichment tools have limited proteome-wide analysis...

Another new preprint is out — with it, a proteome-wide solution to study citrullination at scale!
www.biorxiv.org/content/10.1...
If you’ve been following our journey into one of the trickiest PTMs (citrullination), you might be thinking... what about enrichment before MS?

Our Motif-Specific mAbs...
✔ Motif-specific (and sensitive)
✔ Minimal homocitrullination cross-reactivity
✔ Works in real samples
Also? Some commercial Abs didn’t stand a chance. 😉
To try? We’re making ours openly available to support the citrullination community!
#Citrullination #Antibodies #PTMs

Development of Motif-Specific Monoclonal Antibodies for Global Protein Citrullination Detection with Minimal Cross-Reactivity to Homocitrullination Protein citrullination, a post-translational modification (PTM) catalyzed by peptidylarginine deiminases (PADs), plays critical roles in biological processes such as immunity, gene regulation, and inf...

New preprint! 🎉
www.biorxiv.org/content/10.1...
If you've ever tried detecting citrullinated proteins, you know the pain—most pan-citrullination antibodies are either useless, cross-reactive, or heartbreakingly bad. 💔😭
I tested them. I suffered. I cried. So we made our own.

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...

🚀 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)

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...

🎉 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)

oktoberfest/tutorials at development · wilhelm-lab/oktoberfest Rescoring and spectral library generation pipeline for proteomics. - wilhelm-lab/oktoberfest

We developed a deep learning model to predict MS2 spectra of citrullinated peptides, improving site ID by up to 14x in human tissue proteomes with high precision!
Pipeline available via oktoberfest: github.com/wilhelm-lab/...

Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes Citrullination is a critical yet understudied post-translational modification (PTM) implicated in various biological processes. Exploring its role in health and disease requires a comprehensive unders...

Kicking off the new year strong! Prosit-Cit is officially online!🍻 Check it out: www.mcponline.org/article/S153...

#DeepLearning #Citrullination #Bioinformatics