Mann Lab
@mannlab.bsky.social
The Mann Lab is a pioneer in mass spectrometry-based proteomics. Posts represent personal views from lab members and Matthias Mann
We compared 3 MS and 1 aptamer proteomics workflows on elite athlete plasma. Platform differences aren't just technical—they reveal distinct biology of exercise adaptation and metabolic health. New preprint just in time for Winter Olympics 🏆 🥇
biorxiv.org/content/10.6...
biorxiv.org/content/10.6...
biorxiv.org
February 9, 2026 at 8:10 AM
We compared 3 MS and 1 aptamer proteomics workflows on elite athlete plasma. Platform differences aren't just technical—they reveal distinct biology of exercise adaptation and metabolic health. New preprint just in time for Winter Olympics 🏆 🥇
biorxiv.org/content/10.6...
biorxiv.org/content/10.6...
Discovery proteomics → clinical diagnostics? ADAPT-MS makes it possible by adapting to each sample's protein coverage on-the-fly. No imputation, no fixed panels, multiple diagnostic questions from one measurement. Out now in @natcomms.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An adaptive, continuous-learning framework for clinical decision-making from proteome-wide biofluid data - Nature Communications
Discovery proteomics offers deep insights but is currently not applied clinically in diagnostics. Here, the authors present ADAPT-MS, a flexible machine learning framework that enables fast, personali...
www.nature.com
January 28, 2026 at 12:54 PM
Discovery proteomics → clinical diagnostics? ADAPT-MS makes it possible by adapting to each sample's protein coverage on-the-fly. No imputation, no fixed panels, multiple diagnostic questions from one measurement. Out now in @natcomms.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Congratulations Dr. Vu!
We warmly congratulate Duc Tung Vu from the @mannlab.bsky.social , who succesfully completed his PhD defense today. After years of hard work the fruits of labor come finally to fruition. Congratulations! 🎉
January 27, 2026 at 6:37 PM
Congratulations Dr. Vu!
Very sad to hear about Peer Bork's untimely passing. I have known him since my time at EMBL in the 1990s - a brilliant mind and wonderful collaborator. His contributions to bioinformatics were transformative. The community has lost a giant.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 19, 2026 at 9:08 AM
Very sad to hear about Peer Bork's untimely passing. I have known him since my time at EMBL in the 1990s - a brilliant mind and wonderful collaborator. His contributions to bioinformatics were transformative. The community has lost a giant.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
Happy Holiday Season!
a red background with the words happy holidays and a christmas tree on it
ALT: a red background with the words happy holidays and a christmas tree on it
media.tenor.com
December 23, 2025 at 1:13 PM
Happy Holiday Season!
Celebrating an incredible 2025 @mannlab.bsky.social!
PhD graduations, prestigious awards including Matthias Mann's
@nationalacademies.org election, launch of innovative methods and bioinformatics tools, and celebrating 20 years
@mpibiochem.bsky.social
mannlabs.github.io/research-hig...
PhD graduations, prestigious awards including Matthias Mann's
@nationalacademies.org election, launch of innovative methods and bioinformatics tools, and celebrating 20 years
@mpibiochem.bsky.social
mannlabs.github.io/research-hig...
MannLabs Research Highlights 2025
Summary of recent advances led by the MannLabs at the MPI for Biochemistry in Munich and the Centre for Proteomics Research in Copenhagen
mannlabs.github.io
December 23, 2025 at 1:13 PM
Celebrating an incredible 2025 @mannlab.bsky.social!
PhD graduations, prestigious awards including Matthias Mann's
@nationalacademies.org election, launch of innovative methods and bioinformatics tools, and celebrating 20 years
@mpibiochem.bsky.social
mannlabs.github.io/research-hig...
PhD graduations, prestigious awards including Matthias Mann's
@nationalacademies.org election, launch of innovative methods and bioinformatics tools, and celebrating 20 years
@mpibiochem.bsky.social
mannlabs.github.io/research-hig...
Congrats to all the well-deserving winners of this year's #JSPAward and a shout-out to Thierry Nordmann @tnordmann.bsky.social for his outstanding research on #TEN published in @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 19, 2025 at 1:47 PM
Congrats to all the well-deserving winners of this year's #JSPAward and a shout-out to Thierry Nordmann @tnordmann.bsky.social for his outstanding research on #TEN published in @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
We can know more than we can tell, but now Al can capture it. Our multimodal agent analyzes lab videos to generate protocols & catch common lab errors. Preserving tacit knowledge in proteomics. Now in @molsystbiol.org @patiskowronek.bsky.social #Google
link.springer.com/10.1038/s443...
link.springer.com/10.1038/s443...
December 16, 2025 at 9:29 AM
We can know more than we can tell, but now Al can capture it. Our multimodal agent analyzes lab videos to generate protocols & catch common lab errors. Preserving tacit knowledge in proteomics. Now in @molsystbiol.org @patiskowronek.bsky.social #Google
link.springer.com/10.1038/s443...
link.springer.com/10.1038/s443...
Reposted by Mann Lab
November 27, 2025 at 3:17 PM
Honored to be included in this reflection on 20 excellent years of MolSystBiol! From our first phosphotyrosine interactome in 2005 to proteome-wide networks - scale has grown exponentially. MS proteomics + AI is transforming systems-level understanding. Exciting times!
embopress.org/doi/pdf/10.1...
embopress.org/doi/pdf/10.1...
embopress.org
November 25, 2025 at 12:44 PM
Honored to be included in this reflection on 20 excellent years of MolSystBiol! From our first phosphotyrosine interactome in 2005 to proteome-wide networks - scale has grown exponentially. MS proteomics + AI is transforming systems-level understanding. Exciting times!
embopress.org/doi/pdf/10.1...
embopress.org/doi/pdf/10.1...
Elegant chemistry and cryo-EM explain the selective Lys8 ubiquitylation. A clear example of how metabolite sensing and the ubiquitin system intersect.
November 17, 2025 at 10:27 AM
Elegant chemistry and cryo-EM explain the selective Lys8 ubiquitylation. A clear example of how metabolite sensing and the ubiquitin system intersect.
Great to see Brenda Schulman’s team post their new bioRxiv paper. MS-based proteomics helped uncover a beautifully simple mechanism: cysteine levels tune metabolism by flipping the inverse stability of LRRC58 and its substrate CDO1.
www.biorxiv.org/content/bior...
www.biorxiv.org/content/bior...
www.biorxiv.org
November 17, 2025 at 10:27 AM
Great to see Brenda Schulman’s team post their new bioRxiv paper. MS-based proteomics helped uncover a beautifully simple mechanism: cysteine levels tune metabolism by flipping the inverse stability of LRRC58 and its substrate CDO1.
www.biorxiv.org/content/bior...
www.biorxiv.org/content/bior...
Fantastic time at #HUPO2025 in Toronto! Congratulations to our talented Early Career researchers! Proud winners: Oeller Marc Oeller🥇 1st Place Poster, Kathrin Korff 🥈 Runner-up Poster, and @carolineweiss.bsky.social 🎤 3-Minute Thesis award! The future of #proteomics research is bright!
November 13, 2025 at 12:01 PM
Fantastic time at #HUPO2025 in Toronto! Congratulations to our talented Early Career researchers! Proud winners: Oeller Marc Oeller🥇 1st Place Poster, Kathrin Korff 🥈 Runner-up Poster, and @carolineweiss.bsky.social 🎤 3-Minute Thesis award! The future of #proteomics research is bright!
If you are at HUPO 2025, catch up with our team @mannlab.bsky.social to hear about our exciting work in single-cell proteomics, immunopeptidomics, spatial proteomics, and the latest advances in mass spectrometry technology!
November 7, 2025 at 1:20 PM
If you are at HUPO 2025, catch up with our team @mannlab.bsky.social to hear about our exciting work in single-cell proteomics, immunopeptidomics, spatial proteomics, and the latest advances in mass spectrometry technology!
In Nature Communications: MS-based proteomics + machine learning to diagnose Lyme neuroborreliosis with 92% accuracy (CSF) and 80% (blood) - paving the way for earlier, less invasive testing.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The diagnostic potential of proteomics and machine learning in Lyme neuroborreliosis - Nature Communications
Researchers incorporate mass spectrometry-based proteomics and machine learning to assess the potential of a less invasive diagnostic approach for Lyme neuroborreliosis, a common nervous system infect...
www.nature.com
October 31, 2025 at 1:06 PM
In Nature Communications: MS-based proteomics + machine learning to diagnose Lyme neuroborreliosis with 92% accuracy (CSF) and 80% (blood) - paving the way for earlier, less invasive testing.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Awesome talk by @erictopol.bsky.social at the Bavarian Academy of Sciences and Humanities (BAdW). A positive and hopeful take on #AI in medicine. Thanks for highlighting #DVP, too 😊
October 29, 2025 at 8:58 AM
Awesome talk by @erictopol.bsky.social at the Bavarian Academy of Sciences and Humanities (BAdW). A positive and hopeful take on #AI in medicine. Thanks for highlighting #DVP, too 😊
AlphaDIA is open-source and free for academic and commercial users. We are currently preparing version 2.0 - stay tuned!
#AlphaDIA #Bioinformatics #DeepLearning #MassSpectrometry
#AlphaDIA #Bioinformatics #DeepLearning #MassSpectrometry
October 22, 2025 at 1:36 PM
AlphaDIA is open-source and free for academic and commercial users. We are currently preparing version 2.0 - stay tuned!
#AlphaDIA #Bioinformatics #DeepLearning #MassSpectrometry
#AlphaDIA #Bioinformatics #DeepLearning #MassSpectrometry
Excited to share AlphaDIA's publication in Nature Biotechnology!
Our open-source DIA framework brings deep learning directly to raw MS data with feature-free processing, transfer learning for any PTM, and performance matching top tools.
www.nature.com/articles/s41...
Our open-source DIA framework brings deep learning directly to raw MS data with feature-free processing, transfer learning for any PTM, and performance matching top tools.
www.nature.com/articles/s41...
AlphaDIA enables DIA transfer learning for feature-free proteomics - Nature Biotechnology
An open-source platform for data-independent acquisition proteomics adapts predicted libraries to experimental settings.
www.nature.com
October 22, 2025 at 1:36 PM
Excited to share AlphaDIA's publication in Nature Biotechnology!
Our open-source DIA framework brings deep learning directly to raw MS data with feature-free processing, transfer learning for any PTM, and performance matching top tools.
www.nature.com/articles/s41...
Our open-source DIA framework brings deep learning directly to raw MS data with feature-free processing, transfer learning for any PTM, and performance matching top tools.
www.nature.com/articles/s41...
How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google.
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
In labs, hands-on expertise is often lost because it's not written down. We leverage multimodal AI agents to capture & share expertise by analyzing video and speech to generate protocols, detect errors, and guide researchers. #AI #TeamMassSpec
📄 Preprint: doi.org/10.1101/2025... 1/🧵
📄 Preprint: doi.org/10.1101/2025... 1/🧵
Multimodal AI agents for capturing and sharing laboratory practice
We present a multimodal AI laboratory agent that captures and shares tacit experimental practice by linking written instructions with hands-on laboratory work through the analysis of video, speech, an...
doi.org
October 9, 2025 at 10:54 AM
How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google.
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
16/
If this interests you:
🔁 Retweet the first post:
bsky.app/profile/mann...
⭐️ Give our github repo a star github.com/MannLabs/scP...
❓ tell us what you are going to do with #scPortrait
If this interests you:
🔁 Retweet the first post:
bsky.app/profile/mann...
⭐️ Give our github repo a star github.com/MannLabs/scP...
❓ tell us what you are going to do with #scPortrait
September 24, 2025 at 1:39 PM
16/
If this interests you:
🔁 Retweet the first post:
bsky.app/profile/mann...
⭐️ Give our github repo a star github.com/MannLabs/scP...
❓ tell us what you are going to do with #scPortrait
If this interests you:
🔁 Retweet the first post:
bsky.app/profile/mann...
⭐️ Give our github repo a star github.com/MannLabs/scP...
❓ tell us what you are going to do with #scPortrait
15/
This work was a fantastic collaboration:
@mannlab.bsky.social
@fabiantheis.bsky.social
@v-hornung.bsky.social
A big shoutout to all of our co-authors: Alessandro Palma,
Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova, Mahima Arunkumar, @lukasheumos.bsky.social, @georgwa.bsky.social
This work was a fantastic collaboration:
@mannlab.bsky.social
@fabiantheis.bsky.social
@v-hornung.bsky.social
A big shoutout to all of our co-authors: Alessandro Palma,
Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova, Mahima Arunkumar, @lukasheumos.bsky.social, @georgwa.bsky.social
September 24, 2025 at 1:34 PM
15/
This work was a fantastic collaboration:
@mannlab.bsky.social
@fabiantheis.bsky.social
@v-hornung.bsky.social
A big shoutout to all of our co-authors: Alessandro Palma,
Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova, Mahima Arunkumar, @lukasheumos.bsky.social, @georgwa.bsky.social
This work was a fantastic collaboration:
@mannlab.bsky.social
@fabiantheis.bsky.social
@v-hornung.bsky.social
A big shoutout to all of our co-authors: Alessandro Palma,
Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova, Mahima Arunkumar, @lukasheumos.bsky.social, @georgwa.bsky.social
14/
Bottom line:
scPortrait turns microscopy images into a first-class modality for machine learning and multimodal foundation models, alongside RNA and proteomics 🔬💻
🔗 Preprint: doi.org/10.1101/2025...
🔗 GitHub: github.com/MannLabs/scP...
Bottom line:
scPortrait turns microscopy images into a first-class modality for machine learning and multimodal foundation models, alongside RNA and proteomics 🔬💻
🔗 Preprint: doi.org/10.1101/2025...
🔗 GitHub: github.com/MannLabs/scP...
scPortrait integrates single-cell images into multimodal modeling
Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are accessi...
doi.org
September 24, 2025 at 12:22 PM
14/
Bottom line:
scPortrait turns microscopy images into a first-class modality for machine learning and multimodal foundation models, alongside RNA and proteomics 🔬💻
🔗 Preprint: doi.org/10.1101/2025...
🔗 GitHub: github.com/MannLabs/scP...
Bottom line:
scPortrait turns microscopy images into a first-class modality for machine learning and multimodal foundation models, alongside RNA and proteomics 🔬💻
🔗 Preprint: doi.org/10.1101/2025...
🔗 GitHub: github.com/MannLabs/scP...
13/
Our extensive documentation and tutorials make scPortrait easy to use and accessible.
And as part of @scverse.bsky.social it’s compatible with existing tools like scanpy, squidpy, bento-tools or Moscot 🚀🐍
mannlabs.github.io/scPortrait/i... #OpenSourceTools #Tutorial #CodeDocumentation
Our extensive documentation and tutorials make scPortrait easy to use and accessible.
And as part of @scverse.bsky.social it’s compatible with existing tools like scanpy, squidpy, bento-tools or Moscot 🚀🐍
mannlabs.github.io/scPortrait/i... #OpenSourceTools #Tutorial #CodeDocumentation
September 24, 2025 at 12:22 PM
13/
Our extensive documentation and tutorials make scPortrait easy to use and accessible.
And as part of @scverse.bsky.social it’s compatible with existing tools like scanpy, squidpy, bento-tools or Moscot 🚀🐍
mannlabs.github.io/scPortrait/i... #OpenSourceTools #Tutorial #CodeDocumentation
Our extensive documentation and tutorials make scPortrait easy to use and accessible.
And as part of @scverse.bsky.social it’s compatible with existing tools like scanpy, squidpy, bento-tools or Moscot 🚀🐍
mannlabs.github.io/scPortrait/i... #OpenSourceTools #Tutorial #CodeDocumentation
12/
scPortrait already scales:
1️⃣ 120M+ single-cell images from image-based genetic screens
2️⃣ applied on patient-derived datasets to perform AI-driven morphology analysis
Refs:
1️⃣ BioRxiv2023 ➡️ www.biorxiv.org/content/10.1...
2️⃣ Nature 2025➡️ www.nature.com/articles/s41...
scPortrait already scales:
1️⃣ 120M+ single-cell images from image-based genetic screens
2️⃣ applied on patient-derived datasets to perform AI-driven morphology analysis
Refs:
1️⃣ BioRxiv2023 ➡️ www.biorxiv.org/content/10.1...
2️⃣ Nature 2025➡️ www.nature.com/articles/s41...
SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes
Forward genetic screening associates phenotypes with genotypes by randomly inducing mutations and then identifying those that result in phenotypic changes of interest. Here we present spatially resolv...
www.biorxiv.org
September 24, 2025 at 12:22 PM
12/
scPortrait already scales:
1️⃣ 120M+ single-cell images from image-based genetic screens
2️⃣ applied on patient-derived datasets to perform AI-driven morphology analysis
Refs:
1️⃣ BioRxiv2023 ➡️ www.biorxiv.org/content/10.1...
2️⃣ Nature 2025➡️ www.nature.com/articles/s41...
scPortrait already scales:
1️⃣ 120M+ single-cell images from image-based genetic screens
2️⃣ applied on patient-derived datasets to perform AI-driven morphology analysis
Refs:
1️⃣ BioRxiv2023 ➡️ www.biorxiv.org/content/10.1...
2️⃣ Nature 2025➡️ www.nature.com/articles/s41...
11/
We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler
We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler
September 24, 2025 at 12:22 PM
11/
We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler
We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler