I didn’t know this was already existing

@pride-ebi.bsky.social

Nice! I just mentioned that this feature would be great to have in the PSI-AI meeting. There we have it! I‘ll try it soon thanks!

MCP-Support

Release 3.1.0 - Lustnau · nf-core/epitopeprediction 3.1.0 - Lustnau - 2025-11-19 Added #304 Added --binder_only parameter to filter out non-binding peptides from the final results #306 Added nf-co2footprint plugin Fixed #290 Fixed an issue where ...

Pipeline release! nf-core/epitopeprediction v3.1.0 - 3.1.0 - Lustnau!

Please see the changelog: https://github.com/nf-core/epitopeprediction/releases/tag/3.1.0

Excited to share our new paper “MHCquant2 refines immunopeptidomics tumor antigen discovery” in Genome Biology!
An open-source @nf-co.re workflow using OpenMS, DeepLC & MS²PIP boosts peptide ID & sensitivity. Scalable, reproducible & ready for large-scale immunopeptidomics.

👉 rdcu.be/eHFTZ

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.

There is such a need to harmonize proteomics data, it’s not even funny anymore. pubs.acs.org/doi/full/10....

Pipeline release! nf-core/hlatyping v2.1.0 - 2.1.0 - Chewbacca!

Please see the changelog: https://github.com/nf-core/hlatyping/releases/tag/2.1.0

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework Author summary We have created nf-core/airrflow, a workflow to help researchers study the immune system in healthy and disease states, such as infections, autoimmunity, and cancer. The adaptive immune...

Do you analyze large BCR and TCR sequencing datasets?

Answer our survey for improving nf-core/airrflow, a Nextflow pipeline to analyze bulk and single-cell AIRRseq data (doi.org/10.1371/jour...). We’re interested in your opinion on useful new features!

yalesurvey.ca1.qualtrics.com/jfe/form/SV_...

nf-core/detaxizer nf-co.re/detaxizer: A Benchmarking Study for Decontamination from Human Sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪 nextflow github.com/nf-core/deta...

a cat is sitting in front of a laptop computer on a couch . ALT: a cat is sitting in front of a laptop computer on a couch .

Interested in contributing to @nf-co.re or improving your nf-core pipeline? Register and join the #nf-core hackathon local hub in Tübingen on March 24th-27th if you live nearby! We have snacks and stickers!
nf-co.re/events/2025/...

TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore pubs.acs.org/doi/10....

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#proteomics #prot-paper

We are #hiring! 🚀 Join our #bioinformatics team in a truly #interdisciplinary environment driving #immunopeptidomics analyses and pipeline development with direct impact on advancing patient treatment! Check out the full job description: jobs.medizin.uni-tuebingen.de/Job/5775/Bio...

Audience in lecture hall

Pavel Sinitcyn presenting

Katerina Nastou presenting

Will Fondrie presenting

The EUBIC-MS Developers Meeting 2025 in Brixen is off to a great start with keynotes by Pavel Sinitcyn, Katerina Nastou, and @willfondrie.com.

#EuBIC2025

Can’t stress enough about having some code repository (GitHub etc) especially if you are early career and/or looking for a job. If the selection criteria asks for scientific programming skills, everyone claims they can code and use good practice. Show some evidence by providing a link to GitHub etc

Great Stuff! Thanks for the Thread. Is synchro-PASEF now built-in the Bruker software, or is a Special plugin needed?

Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics Data-independent acquisition (DIA) on ion mobility mass spectrometers enables deep proteome coverage and high data completeness in large-scale proteomics studies. For advanced acquisition schemes such...

Nice and short technical paper about how air pressure can change ion mobility shifts and peptide quantification! #proteomics
pubs.acs.org/doi/abs/10.1...

I was forced to do 3h pure copy&pasting excel lists as a student assistant and got sick of it quickly

Frontiers | Warehouse-based, immunopeptidome-guided design of personalised peptide vaccines shows feasibility in clinical trial evaluation in CLL patients

Phase I trial update: Our warehouse-based cancer peptide vaccine for CLL showed promising safety but limited T cell responses.
Next: Follow-up trial with improved adjuvants & BTK inhibitors underway. Stay tuned! #CancerResearch #Immunopeptidomics #Immunotherapy
🔗 doi.org/10.3389/fimm...

Nice tiny Xmas gift in the new release 🎄. Percolator feature weights can be simply plotted now with multiQC!

Leveraging the Human Panproteome to Enhance Peptide and Protein Identification in Proteomics and Metaproteomics www.biorxiv.org/cont...

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#proteomics #prot-preprint

Nice work! I had a hard time using some of these tools with #immunopeptidomics data some time ago. Do you know/recommend a tool here that is decent in analyzing this data?

Happy to announce MS²Rescore v3.0, our much-improved platform for #MachineLearning driven rescoring of #Proteomics search results.

A big thanks to Louise Buur and Viktoria Dorfer for the great collaboration!

Open access full text: biblio.ugent.be/publication/...
Project: github.com/compomics/ms...

Pipeline release! nf-core/epitopeprediction v2.3.0 - 2.3.0 - Oesterberg!

Please see the changelog: https://github.com/nf-core/epitopeprediction/releases/tag/2.3.0