Chemoproteomics is back at #ASMS2026 with a bang! After the oral session mysteriously vanished last year, now we're not only back on the schedule but kicking off the conference with Ben Cravatt?! 1/n
Florian P Bayer
@flobayer.bsky.social
PhD student in PTM proteomics @kusterlab
Proteoforms as the true units of physiological function link.springer.com/ar... --- #proteomics #prot-paper
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:
Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome
Mass-spectrometry-based phosphoproteomics enables the analysis of thousands of protein phosphorylation events across the human proteome. However, there is a lack of scalable, hypothesis-free, and stat...
doi.org
Very happy to see that dose-response curves are now super easy to access for everyone in proteomicsDB. Just a few clicks and you can see at which concentrations your favorite drug engages protein target(s), tinkers with signaling pathways, and inhibits cell growth. Read more: doi.org/10.1093/nar/...
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Abstract. Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanism
doi.org
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
A very clever approach to learn and predict MS2 spectra for modified peptides. By augmenting modification encodings and combining them with PROSIT, the new model has essentially generalized to ANY PTM - not just those in the training dataset. Super exciting !!
AI x Bio Discovery@aixbiobot.bsky.social · 11mo agoLearning the Unseen: Data-Augmented Deep Learning for PTM Discovery with Prosit-PTM [new] Data-augmented DL enables zero-shot PTM prediction, improving site ID & localization in proteomics.
Very excited to see this story out in Science Signaling!! Especially the use of dose-dependent profiling at different time points could clearly separate immediate from late and consequential signaling changes in KRAS-driven (phospho)proteomes.
Kusterlab@kusterlab.bsky.social · last yr.Excited to share our latest work published in #ScienceSignaling! 🚀 www.science.org/doi/10.1126/... (1/4)
Assessing error control is fundamental in mass spectrometry-based proteomics. @bo-wen.bsky.social @maccoss.bsky.social @urikeich.bsky.social et al introduce a theoretical foundation for entrapment along with a method for more accurate evaluation of FDR control. 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...
nature.com
I am looking forward to discuss with with you: • (phospho)proteome-wide dose-response profiling • statistical analysis of 180 million curves with CurveCurator • mapping kinase-resolved activities changes due to all target engagements • (re-)evaluating the kinase substrate space in humans
Kusterlab@kusterlab.bsky.social · last yr.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!
🚨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
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
🚀 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
That is precisely why we are doing high-throughput, dose-dependent, (PTM)proteome-wide analyses to study MOAs of inhibitors, cell signaling, and cell adaptions. There is such a mess in the literature caused by either low throughput or single-dose perturbation experiments. That needs to be solved!
Nikolai Slavov@slavov-n.bsky.social · 2y agoA common problem is that high-throughput data (and models) often focus on what can be easily measured at high-throughput rather that what should be measured (and modeled) to answer scientific questions. Just scaling up is not enough. nikolai.slavovlab.net/high-through...
A very nice implementation of magnetic beads based competition pull-downs with DIA readout. This workflow is well suited for real throughput … CurveCurator is the perfect match for fast and reliable statistical analysis of these dose-response data sets.
PastelBio@pastelbio.bsky.social · 2y agoAutomated High-Throughput Affinity Capture-Mass Spectrometry Platform with Data-Independent Acquisition pubs.acs.org/doi/10.... --- #proteomics #prot-paper
Drug synergy is a fascinating phenomenon where 1+1=3. But what molecular mechanisms drive this effect? Our dose-resolved combination treatments with (phospho)proteome-wide readouts provide unprecedented quantitative detail of the DNA damage response. Read more: www.embopress.org/doi/full/10....
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...
embopress.org
A very cool new tool to make sense out of proteome-wide perturbation data from a pathway perspective is now integrated in proteomicsDB. Especially decryptM data can be visualized well to see drug potencies for each p-site across a pathway of proteins. Check it out !!
Kusterlab@kusterlab.bsky.social · 2y ago🎉 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)