MHCquant2 refines immunopeptidomics tumor antigen discovery
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
24.09.2025 20:20 — 👍 5 🔁 1 💬 0 📌 0
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....
06.10.2025 07:30 — 👍 0 🔁 0 💬 0 📌 0
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
14.04.2025 15:11 — 👍 2 🔁 1 💬 0 📌 0
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...
31.03.2025 10:01 — 👍 12 🔁 6 💬 0 📌 0
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/...
28.02.2025 14:50 — 👍 3 🔁 0 💬 0 📌 0
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
07.02.2025 08:20 — 👍 1 🔁 1 💬 0 📌 0
Bioinformatician (f/m/d)
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...
04.02.2025 06:43 — 👍 0 🔁 1 💬 0 📌 0
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
03.02.2025 12:59 — 👍 23 🔁 11 💬 1 📌 0
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
01.02.2025 09:13 — 👍 41 🔁 15 💬 2 📌 0
Great Stuff! Thanks for the Thread. Is synchro-PASEF now built-in the Bruker software, or is a Special plugin needed?
28.01.2025 13:40 — 👍 0 🔁 0 💬 1 📌 0
I was forced to do 3h pure copy&pasting excel lists as a student assistant and got sick of it quickly
14.01.2025 22:38 — 👍 0 🔁 0 💬 0 📌 0
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...
08.01.2025 12:18 — 👍 6 🔁 1 💬 0 📌 0
Nice tiny Xmas gift in the new release 🎄. Percolator feature weights can be simply plotted now with multiQC!
22.12.2024 11:50 — 👍 3 🔁 1 💬 0 📌 0
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
27.11.2024 08:40 — 👍 4 🔁 4 💬 0 📌 0
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?
23.11.2024 08:46 — 👍 0 🔁 0 💬 1 📌 0
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
26.02.2024 11:52 — 👍 3 🔁 2 💬 0 📌 0
Professor of Experimental Immunology at the University of Tübingen, M3 Research Center & Institute of Immunology. 🧪🔬 Interested in immunity in cancer and infection. Fascinated by dendritic cells, T cells and NK cells
Scientist exploring immune cell dynamics across scales. Passionate about microscopy - live-cell, intravital, and light-sheet imaging - and linking cellular functions in tissues to systemic effects.
A platform for life sciences. Publications, research protocols, news, events, jobs and more. Sign up at https://www.lifescience.net.
Postdoc at the University of Antwerp working on improving the identification rate of immunopeptides in TimsTOF data. Also interested in privacy and post-translational modifications.
Yearly Bioinformatics Open Source Conference since 2000, run by @OpenBio.
BOSC 2026 will be between July 12-16, 2026, as part of ISMB 2026
BOSC 2025 was July 21-22, 2025, in Liverpool, UK as part of ISMB/ECCB 2025
https://www.open-bio.org/events/bosc/
We read papers, so you'll want to, too.
An unholy amalgation of T cell tamer @dlwagner.bsky.social and kidney lover @lostendorf.bsky.social
Computational Immunologist @Yale School of Medicine
The American Society for Mass Spectrometry was established in 1969. We serve the mass spec community with in-person research conferences, awards & recognition programs, various online offerings, and more. Learn more at https://www.asms.org
The number of people using expensive, black-box software for proteomics is bewildering.
Research group at UNC-Chapel Hill under the direction of Dr. Erin S. Baker & focused on ion mobility-mass spectrometry research for biological and environmental systems.
🔬👩🔬 VIB researchers explore the basic molecular mechanisms of life, from microorganisms to plants and human beings. Our entrepreneurial technology transfer approach ensures that scientific discoveries are turned into tangible innovations.
vib.be
PhD student in computational proteomics
Measurements want to be accurate;
Experiments want to be elegant;
Data wants to be beautiful and Data wants to be free
#proteomics
#rstats
Europe PMC provides comprehensive access to life sciences literature from trusted sources. It's available to anyone, anywhere for free. https://europepmc.org/
AI & Proteomics Researcher @ MannLab - Max Planck Institute | PhD Biochemistry | Bioinformatics | Mass Spectrometry Expert | Automating complex workflows in life sciences
