Johannes Zimmermann

🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1

Predicting protein-protein interactions in the human proteome Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identificatio...

Predicting protein-protein interactions.

They '...systematically screened 200 million human protein pairs and predicted 17,849 interactions with anexpected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens.'

www.science.org/doi/epdf/10....

🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳

📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org

OmniPath integrates 160+ resources for multi-omics analysis & modeling.

🧶⬇️

Abuse of power at universities is a problem in many countries. Unfortunately, the open to read book is just available in German language.

If you are a #PhD candidate or #student in the fields of #Biochemistry or #ChemBio and would like to go to the #Biochemistry2026 conference in Würzburg, consider applying for the brand new @gdchbiochem.bsky.social Meeting #Award!

en.gdch.de/network-stru...
#ChemSky #ECR #EarlyCareerResearcher

It's maybe just anecdotal but we moved our QE plus from Freiburg to Würzburg in a new lab. And even after an exploded split flow it's remarkable stable for 10-14 days.

I still find it super curious how different the performance can be. And that their are still gains in precision manufacturing for an already well understood component like the Orbitrap.

Major part of my PhD thesis is finally online! Thanks to everyone involved 🙏 @walterwchen.bsky.social @rjdlab.bsky.social @tmoeckli.bsky.social @hirakdas.bsky.social and the entire @warscheidlab.bsky.social #peroxisomes #Massspec #proteomics

Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling Proteomic analyses offer insights into how KRAS inhibitors affect oncogenic KRAS signaling.

Excited to share our latest work published in #ScienceSignaling! 🚀
www.science.org/doi/10.1126/...
(1/4)

On our Orbitrap systems, we normally limit the mass range to 1200m/z in DDA, so I can not give feedback. But still shared your post for better visibility. Hopefully, somebody can help.

When analysing peptides from in-gel digests by LC-MS/MS, has anyone noticed a 1+ ion of m/z 1342.93 after washing the column with 80% ACN? We are leaving the pump at 80% ACN at 1uL/min for 5 mins after our usual 0-40% ACN gradient. Doesn't correspond to any contaminants. #massspechelp

PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...

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#proteomics #prot-paper

Jesper Olsen Lab (Guzman et al) independently reproduces MAP-MS (eDR) proteome depth and compares Astral Zoom MS to the older model.

"...yielding ~15,000 and ~30,000 additional precursors..."

eDR: www.biorxiv.org/content/10.1...
MAP-MS: www.biorxiv.org/content/10.1...

As Requested - A Starter Pack of PIs in Biology (or adjacent) fields who are recruiting POSTDOCS! Please don't hesitate to reach out if you wish to be added! go.bsky.app/4gbXXR3

▶️▶️ To all mass spec enthusiasts: A postdoc position (three years) is available in our international group. Please apply if you are interested in structural MS and in developing novel cross-link ing MS workflows!🧪
Thanks @diegofgar.bsky.social for sharing!
#teammassspec
#AcademicSky
#ChemSky

Check out our newest paper (tinyurl.com/scp-ms) straight from the lab of @erwinschoof.bsky.social. If you are considering to FAIMS or not to FAIMS and whether wide or narrow window DIA is better, you might find some answers you are looking for. #proteomics

🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here!

💡 Create stunning, shareable HTML reports for your collaborators in seconds.

✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC

📣📣It is great to finally welcome @cnicproteomics.bsky.social to Bluesky 🎊 Follow them if you want to learn about the latest development in PTM research applied to cardiovascular diseases! 🫀🧪🧫🖥️🛠️

GitHub - pwilmart/quantitative_proteomics_comparison: Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies - pwilmart/quantitative_proteomics_comparison

DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before:
github.com/pwilmart/qua...

Skeletal muscle proteomics: considerations and opportunities npj Metabolic Health and Disease - Skeletal muscle proteomics: considerations and opportunities

Are you interested in #proteomics and #skeletalmuscle? It can be a real pain to get deep reproducible coverage. Check out our review with @adeshmukh.bsky.social We analyse some considerations including current limitations and how to potentially overcome them #myoblue @unimelbcmr.bsky.social

🚀🚀 🚀 Exciting News! 🚀 🚀 🚀

After more than 4.5 fantastic years at @embl.org, I am excited to announce that from 1 August 2025, I’ll be starting my own research group at Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany — as part of the Biochemistry Department [1/n]

MaxQuant Summer School 2025 (Utrecht, Netherlands) 16th International Summer School On Computational Mass Spectrometry-Based Proteomics

⏳ Just 1 week left to register for MaxQuant Summer School 2025!
📅 Registration closes: July 7
📍 Utrecht, July 21–25
💻 Hands-on training in MaxQuant, Perseus & mass-spectrometry-based proteomics
🔗 Sign up now: eventbrite.de/e/maxquant-s...
🌐 Details: maxquant.org/summer_school/
#TeamMassSpec

Anyone interested in using mass spectrometry to identify and quantify peptides and proteins in plasma, tissue and organoid cell systems?

I have a Research Assistant position in my lab at the Institute of Metabolic Science - Metabolic Research Laboratories.

Apply here:

lnkd.in/dCxhS3GN

Update of our protein outlier caller PROTRIDER. We now handle missing values, a widespread issue for mass spec where missing values are not a random -- and this improves outlier detection on non-missing data! Thumbs up to Daniela and George for the great work.
doi.org/10.1101/2025...

🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets

Meet the Team and Labs behind the project
👉 quantms.org/about

#OpenSource #Proteomics #ASMS2025

Evaluation of an Orbitrap Astral Zoom mass spectrometer prototype for quantitative proteomics - beyond identification lists Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

Astral Zoom, here's the preprint with detailed comparison to the Astral: doi.org/10.1101/2025...

Almost intentionally, looks like all of the new Thermo instrument pages are up (Astral Zoom, Excedion Pro, Optispray).
Overall vibes?
Excedion is the bigger upgrade, almost 2x faster and can now do ETD. Astral Zoom improvements are more incremental.
No change to instrument sensitivity specs.

Very excited that another chapter of my PhD is finally out! 🎉 We compared methods to infer kinase activities from #phosphoproteomics data so check it out if that sounds interesting to you. More details in the thread below 🧵👇🏼

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...

🚨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...

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