Florian P Bayer
@flobayer.bsky.social
PhD student in PTM proteomics @kusterlab
Reposted by Florian P Bayer
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 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...
www.nature.com
November 11, 2025 at 8:06 PM
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 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...
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 !!
Learning 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.
Data-augmented DL enables zero-shot PTM prediction, improving site ID & localization in proteomics.
November 11, 2025 at 5:14 PM
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 !!
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.
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.
Excited to share our latest work published in #ScienceSignaling! 🚀
www.science.org/doi/10.1126/...
(1/4)
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
July 31, 2025 at 11:10 AM
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.
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.
Reposted by Florian P Bayer
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...
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 4:46 PM
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...
www.nature.com/articles/s41...
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
• (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
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!
Go #TeamMassSpec!
June 4, 2025 at 11:00 AM
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
• (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
Reposted by Florian P Bayer
🚨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...
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
May 22, 2025 at 6:44 PM
🚨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...
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...
Reposted by Florian P Bayer
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
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
April 22, 2025 at 11:44 AM
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
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
Reposted by Florian P Bayer
🚀 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
March 4, 2025 at 4:06 PM
🚀 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)
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!
There is such a mess in the literature caused by either low throughput or single-dose perturbation experiments. That needs to be solved!
A 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...
Just scaling up is not enough.
nikolai.slavovlab.net/high-through...
February 23, 2025 at 10:22 AM
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!
There is such a mess in the literature caused by either low throughput or single-dose perturbation experiments. That needs to be solved!
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.
CurveCurator is the perfect match for fast and reliable statistical analysis of these dose-response data sets.
Automated High-Throughput Affinity Capture-Mass Spectrometry Platform with Data-Independent Acquisition pubs.acs.org/doi/10....
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#proteomics #prot-paper
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#proteomics #prot-paper
January 27, 2025 at 11:08 PM
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.
CurveCurator is the perfect match for fast and reliable statistical analysis of these dose-response data sets.
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....
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...
www.embopress.org
January 22, 2025 at 12:58 AM
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....
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....
🎉🎉🎉
Congratulations to Prof. Bernhard Küster on being selected as the 2025 Karger Medal Recipient.
Join us for a celebration on Monday, March 10 !
cos.northeastern.edu/barnett/abou...
Join us for a celebration on Monday, March 10 !
cos.northeastern.edu/barnett/abou...
January 20, 2025 at 8:36 PM
🎉🎉🎉
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 !!
Especially decryptM data can be visualized well to see drug potencies for each p-site across a pathway of proteins.
Check it out !!
🎉 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)
📄 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
January 10, 2025 at 4:36 PM
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 !!
Especially decryptM data can be visualized well to see drug potencies for each p-site across a pathway of proteins.
Check it out !!