Mann Lab

Congratulations to first author Jakob Bader and thanks to our wonderful collaborators Bernhard Hemmer, Christiane Gasperi @tum.de and the entire team!

Beyond diagnosis, the CSF proteome at diagnosis informs disability progression and disease course evolution years later — a major unmet need in MS. At ~2,000 proteins per sample, proteomics is becoming a powerful engine for biomarker discovery in neurology, for MS and beyond.

For multiple sclerosis, we focused on the ~10% of patients lacking oligoclonal bands, where diagnosis is hardest. Our 22-protein panel outperforms current CSF parameters for differential diagnosis from other inflammatory CNS diseases — validated with a targeted assay.

Now in @cellpress.bsky.social: We profiled cerebrospinal fluid proteomes from 5,000 neurology patients by mass spectrometry — mapping protein changes across stroke, brain cancer, infections & autoimmune diseases, revealing shared and disease-specific signatures.
www.sciencedirect.com/science/arti...

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Curious to see where the combination of single-cell resolution and spatial context in proteomics will take us next! Congrats to @carolineweiss.bsky.social , @poratshliomlab.bsky.social and team at the NCI and Karsten Borgwardt and team @mpibiochem.bsky.social

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We also examined liver tissue with disrupted architecture (desmoplasia). Protein zonation is globally reduced, but pericentral proteins are hit hardest. Only 11.6% maintained their zonation vs. 41.2% for portal vein proteins.

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How conserved is liver zonation between species? Re-analyzing our mouse scDVP data with the same framework showed: core metabolic functions are conserved, but ribosomal proteins show periportal enrichment only in humans - reflecting higher protein synthesis demands in oxygen-rich regions?

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~47% of the proteome is zonated. 171 proteins show particularly strong spatial gradients. Explore any protein yourself: human-liver-dvp.streamlit.app

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(2) A continuous gradient analysis assigning each protein a quantitative zonation coefficient - no binning required.

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Two key developments made this possible: (1) CellPick (cellpick.app) — a strategic cell selection framework maximizing spatial coverage per section, now a general tool for spatial (prote)omics.

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Liver divides labor spatially. Hepatocytes near portal veins perform different metabolic functions than those near central veins, known as liver zonation. Disrupted zonation are hallmarks of liver disease. A comprehensive protein-level map of human liver zonation was lacking. We provide one.

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18 individuals - 800 cells - 2,500+ proteins per cell. First author @carolineweiss.bsky.socialexplains further below.

Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture - Nature Metabolism Using the single-cell Deep Visual Proteomics technique, the authors develop a resource providing spatially resolved proteomic analysis of individual cells in human liver tissue.

Ever wondered how the human liver looks like at single-cell, spatial protein resolution? We used single-cell Deep Visual Proteomics to map human liver zonation at the protein level - one hepatocyte at a time. Our paper is out in @natmetabolism.nature.com! www.nature.com/articles/s42...

He was a visionary who helped make Denmark a powerhouse in proteomics and built a legacy through the many scientists he trained. Rest in peace, Peter.

Obituary for Peter Roepstorff Professor Peter Roepstorff passed away on 3 February 2026 at the age of 83. Thus ended a long research career focused on mapping the functions of proteins in living organisms.

Peter Roepstorff, one of the founding figures of biological mass spectrometry, has passed away at 83. As my postdoc advisor at the University of Southern Denmark, he showed me early on what MS could do for understanding proteins. sdunet.dk/en/enheder/i...

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...

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...

Congratulations Dr. Vu!

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.

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...

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

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...

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...

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...

We congratulate @georgwa.bsky.social from the @mannlab.bsky.social on his sucessful #PhD defense!

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...

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...

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!

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...

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...