iiinova — where your digital self keeps evolving

Mann Lab @mannlab.bsky.social · 06/10/2026

400,000 citations! 🎉 Matthias Mann @mannlab.bsky.social just crossed this remarkable milestone on Google Scholar. From electrospray to MaxQuant to Deep Visual Proteomics, he has shaped how the world does proteomics. Congratulations from your team! #Proteomics scholar.google.com/citations?us...

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Mann Lab @mannlab.bsky.social · 05/10/2026

That's a wrap on #HUPO2026 Singapore! 🎉 Congrats to Katherine Madden (🥇 Poster Competition), Elena Kratz (runner-up) & Kathrin Korff (Thesis Competition runner-up). And to alumni Jesper Olsen, Akhilesh Pandey & Florian Rosenberger, & to Judith Steen, on their HUPO awards! 👏

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Mann Lab @mannlab.bsky.social · 25/09/2026

At #HUPO2026? Come say hi to some of our @mannlab.bsky.social teammates👋 — talks & posters all week on spatial proteomics, plasma biomarkers, a human cell-type proteome atlas, interactomics & AI-driven peptide sequencing. Plenary by Matthias Mann Wed 9:00!

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Mann Lab @mannlab.bsky.social · 15/09/2026

Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome and spatial data live in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native. doi.org/10.64898/202...

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Mann Lab @mannlab.bsky.social · 12/06/2026

That's a wrap for ASMS 2026 for @mannlab.bsky.social team mates. The science on display was genuinely outstanding, and seeing where the field is heading has left us more motivated than ever to keep pushing our own work forward. Until next time! #ASMS2026 #MassSpectrometry #proteomics

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Mann Lab @mannlab.bsky.social · 31/05/2026

At ASMS 2026? Come say hi to the MannLabs team — six talks & posters across the week on single-cell proteomics, interactome profiling, PTM enrichment, deep-learning targeted proteomics, and the latest in mass spec technology. #ASMS2026 #Proteomics #MassSpec #SingleCellProteomics

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Mann Lab @mannlab.bsky.social · 19/03/2026

The legendary Tom Cech delivered a masterful distinguished lecture @mpibiochem.bsky.social on how RNA controls DNA. The audience was captivated! Tom's infectious energy, humility and groundbreaking science continue to inspire us all. Thanks so much for your memorable visit!

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Mann Lab @mannlab.bsky.social · 25/02/2026

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.

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Mann Lab @mannlab.bsky.social · 25/02/2026

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.

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Mann Lab @mannlab.bsky.social · 25/02/2026

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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Mann Lab @mannlab.bsky.social · 20/02/2026

5/ 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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Mann Lab @mannlab.bsky.social · 20/02/2026

4/ 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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Mann Lab @mannlab.bsky.social · 20/02/2026

3c/ ~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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Mann Lab @mannlab.bsky.social · 20/02/2026

2/ 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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Mann Lab @mannlab.bsky.social · 19/12/2025

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...

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Mann Lab @mannlab.bsky.social · 13/11/2025

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!

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Mann Lab @mannlab.bsky.social · 07/11/2025

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!

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Mann Lab @mannlab.bsky.social · 29/10/2025

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 😊

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Mann Lab @mannlab.bsky.social · 24/09/2025

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

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Mann Lab @mannlab.bsky.social · 24/09/2025

11/ We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler

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Mann Lab @mannlab.bsky.social · 24/09/2025

10/ ✨ Embedding images into transcriptome atlases ✨ We use scPortrait to embed single-cell images from a @10xgenomics.bsky.social Xenium ovarian cancer dataset into the #SCimilarity transcriptome atlas (R2 = 0.65), recovering meaningful cell types

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Mann Lab @mannlab.bsky.social · 24/09/2025

9/ ✨ Morphology defined cell states ✨ Image embeddings generated with scPortrait resolve intra- vs extratumoral macrophages with distinct morphologies, linked to anti-inflammatory vs fibroblast-like programs

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Mann Lab @mannlab.bsky.social · 24/09/2025

8/ ✨ Transcriptomes from images ✨ Using optimal transport + flow matching, scPortrait generates gene expression directly from CODEX images, capturing canonical marker expression like TCL1A in germinal centers in the tonsil #CODEX #flowmatching #OT

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Mann Lab @mannlab.bsky.social · 24/09/2025

6/ The new .h5sc format provides fast random access to single-cell images for ML training. It follows #FAIR data principles (findable, accessible, interoperable, reusable) and integrates with @scverse.bsky.social tools via AnnData.

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Mann Lab @mannlab.bsky.social · 24/09/2025

5/ The scPortrait pipeline transforms raw input images step by step: • stitch FOVs • segment & extract cells • output standardized .h5sc single-cell image datasets From messy pixels → inputs ready for training 🖥️

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Mann Lab @mannlab.bsky.social · 24/09/2025

1/ Tomorrow’s large scale cross-modality models will further unlock biology, but they need standardized inputs. With @sophia-maedler.bsky.social & @nik-as.bsky.social, we built #scPortrait, @scverse.bsky.social package to turn microscopy images into single-cell image datasets for multimodal modeling

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Mann Lab @mannlab.bsky.social · 15/09/2025

Congratulations on the inaugural of #AITHYRA, the new Biomedical AI institute in Vienna. Thank you for the invitation to speak at the symposium and the fascinating discussions on AI × proteomics. #AIforLifeScience

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Mann Lab @mannlab.bsky.social · 10/09/2025

Withdrawal of the stem-cell niche WNR (Wnt-Noggin-R-spondin) cocktail in organoid cultures decreased proliferation and stemness, as well as improved differentiation, moving organoids toward more tissue-like states.

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Mann Lab @mannlab.bsky.social · 10/09/2025

scDVP’s high-resolution enabled us to observe fine-grained protein abundance changes along the colon crypt axis. For instance, the abundance gradient of CA1 was only visible in organoid transplants and in vivo tissue.

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Mann Lab @mannlab.bsky.social · 10/09/2025

We further employed scDVP to explore differences in individual intestinal epithelial cells. This dataset comprised about 2,700 proteins across cell types, and confirmed clearer stemness-to-differentiation programs after organoid xenotransplantation.

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Mann Lab @mannlab.bsky.social · 10/09/2025

Led by @freddyomics.bsky.social‬ and @hausmannannika.bsky.social‬, we created a spatial human colon resource consisting of almost 8,000 protein groups across distinct cell types! This reference enabled us to assess cell populations of human colon organoids and establish a colon stemness signature.

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Mann Lab @mannlab.bsky.social · 10/09/2025

Out in @cp-cellsystems.bsky.social‬: Deep Visual Proteomics shows xenotransplantation drives colon #organoids toward in-vivo-like proteomes supporting their use in regenerative medicine; culture tweaks can mimic this shift. With @kimbakjensen.bsky.social. Lead author Frederik Post explains below:

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Mann Lab @mannlab.bsky.social · 13/08/2025

If you are at the ASBMB Proteomics conference next week, do attend the session talks and lunch seminars @abseabio.bsky.social, @evosep.bsky.social to know about the latest research developments in @mannlab.bsky.social

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Mann Lab @mannlab.bsky.social · 26/06/2025

#6: Our integrative approach led to validation of 16 therapeutic targets. Combining Milciclib (CDK inhibitor) with Mirvetuximab (targets FOLR1) significantly reduced tumor burden in vivo—a promising new strategy for treating chemo-resistant LGSC.

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Mann Lab @mannlab.bsky.social · 26/06/2025

#5: For clinical interpretation, we performed a multi-modal data integration – ranging from clinical pathology to the molecular fingerprint of each sample.

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Mann Lab @mannlab.bsky.social · 26/06/2025

#4: Spatial mapping of tumor–stroma interactions revealed how epithelial tumor cells engage their environment—highlighting key roles for integrins and fibronectin in facilitating invasion and matrix remodeling.

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Mann Lab @mannlab.bsky.social · 26/06/2025

#3: Our proteomic profiling of epithelial cells revealed several key mechanisms, including the exclusive expression of the brain-specific splicing regulator NOVA in invasive cancer. A molecular ‘switch’ to invasive tumor growth?

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Mann Lab @mannlab.bsky.social · 26/06/2025

#2: Using cell-type resolved #DeepVisualProteomics, we uncovered a gradual transformation from SBT to LGSC, via micropapillary tumors as a transition state—profiling up to 5,400 proteins from just ~200 cells per sample!

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Mann Lab @mannlab.bsky.social · 26/06/2025

#1: Low-grade serous ovarian cancer (LGSC) is a chemo-resistant and metastasizing disease that affects younger women. We studied its origin by analyzing the progression from serous borderline tumors (SBT) across epithelial and stromal cells.

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Mann Lab @mannlab.bsky.social · 04/06/2025

Don't forget to check out Marvin Thielert's poster 773 on single cell proteomics at #ASMS2025! #SingleCellProteomics

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Mann Lab @mannlab.bsky.social · 02/06/2025

Nano-scale, mega-impact: nanoPhos delivers 100× phosphoproteomics sensitivity, 70k sites from 1µg, 8k from 10ng! Powered by SPEC, it enables phosphoDVP: deep spatial phosphoproteomics from 1000 neurons, hitting 17k sites, a game changer for spatial omics. www.biorxiv.org/content/10.1...

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Mann Lab @mannlab.bsky.social · 01/06/2025

Heading to #ASMS2025? Our team will be there showcasing our latest breakthroughs in mass spectrometry! Don't miss the chance to connect with our team members and discover the cutting-edge work we have been developing.

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Mann Lab @mannlab.bsky.social · 06/05/2025

Check out ADAPT-MS: our flexible, scalable diagnostic framework that transforms discovery plasma proteomics directly into clinical decisions.Dynamic retraining enables single-sample diagnostics for any clinical question. www.medrxiv.org/content/10.1...

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Mann Lab @mannlab.bsky.social · 16/04/2025

Lastly, we achieved up to 4,300 proteins from as little as ⅓ of a single cell! This allowed us to track proteotoxic stress across pseudotime using molecular cartography.

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Mann Lab @mannlab.bsky.social · 16/04/2025

We combined AI-driven morphology analysis with DVP to sample 12,500 hepatocytes by aggregate shape. What we found: (1) Globular aggregates = late-stage, apoptotic phenotype (2) Amorphous aggregates = earlier stress state (3) Morphology reflects molecular fate

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Mann Lab @mannlab.bsky.social · 16/04/2025

Key findings: (1) Early peroxisomal stress response — before the canonical UPR (2) AAT accumulation is cell-intrinsic — minimal stress propagation (3) TNFSF10 marks a late, apoptotic-like hepatocyte state

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Mann Lab @mannlab.bsky.social · 16/04/2025

We teamed up with clinical partners in Aachen, Odense, and Prague to generate spatially resolved proteomes from FFPE liver biopsies across all fibrosis stages (F1–F4). This study was only possible thanks to this fantastic collaboration!

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Mann Lab @mannlab.bsky.social · 16/04/2025

We used DVP — combining imaging, laser microdissection, and ultra-sensitive mass spectrometry. Always a joy to watch individual cells get laser-cut out of their native tissue environment!

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Mann Lab @mannlab.bsky.social · 16/04/2025

AATD is a genetic liver disease caused by misfolded α1-antitrypsin (AAT) aggregating inside hepatocytes. But how exactly do these aggregates harm cells, and how does damage unfold across disease stages? This remained unclear — until now.

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Mann Lab @mannlab.bsky.social · 14/04/2025

Introducing our single-cell DVP framework combining strategic cell selection with protein gradient mapping algorithms. Analyzing hepatocyte proteomes across 18 human livers, revealing cross-species differences, and mapping disruptions in liver fibrosis. www.biorxiv.org/content/10.1...

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