📢 Mark your calendars!
We’re excited to announce the EuBIC-MS 2027 Hackathon!
📍 Gimo, Sweden
📅 31 January – 5 February 2027
💡 Have a hackathon idea?
The call for topic proposals is now open on the EuBIC GitHub repository: github.com/EuBIC/EuBIC2...
We’re looking forward to seeing you there!
Happy to have this one finally out. Since the first generation was very popular in the proteomics community, we decided to work on a second generation including the latest innovations in LC-MS. Very grateful to all collaborators and a special shoutout to @robbedevr.bsky.social from @compomics.com
Monday posters: Caroline Jachman — ‘Gotta catch ’em all: The E. coli pan-proteome PeptideAtlas build, an online protein & PTM pokédex’ (PV.01.087). Friends of HUPO posters: Tine Claeys, Ralf Gabriels, Samuel Wein — ‘HUPO-PSI AI-Readiness Working Group: Advancing FAIR and AI-ready public proteomics data’; Ralf Gabriels — ‘Rusteomics: Bringing the benefits of the Rust programming language to proteomics data analysis’; Ralf Gabriels — ‘EuBIC-MS: A community for collaboration, training, and open development in computational mass spectrometry’; Robbin Bouwmeester — ‘ProteoBench: A community-driven, transparent, and continuously evolving benchmarking platform for mass spectrometry-based proteomics workflows’; Tim Van Den Bossche — ‘The Metaproteomics Initiative.’ Tuesday posters: Toon Callens — ‘Advancing tissue prediction using read-based DNA methylation and metabolomics modeling towards a multi-omics integration’ (PV.02.071); Robbe Devreese — ‘ProteoBench: A community-curated platform for comparison of proteomics data analysis workflows’ (PV.02.102); Enrico Massignani — ‘Exploring functional PTM relationships with MoDPA: A machine learning framework for protein regulation analysis’ (PV.02.108); Sam van Puyenbroeck — ‘The challenge of identification ambiguity in deep learning-based de novo sequencing’ (PV.02.116); Natalia Tichshchenko — ‘Protean: a tool to visualise proteoforms with modifications’ (PV.02.213). Wednesday posters: Tine Claeys — ‘Bridging expert curation and LLMs for automated metadata extraction in lesSDRF 2.0’ (PV.03.007); Alireza Nameni — ‘Enhancing peptide identification with nonlinear models in mokapot: assessing complexity, overfitting, and FDR’ (PV.03.014); Arthur Declercq — ‘MHC-3PO: A hybrid AI prediction framework for modification-aware binding affinity predictions’ (PV.03.057); Pathmanaban Ramasamy — ‘Assessing the relation between protein phosphorylation, AlphaFold3 models, and conformational variability’ (PV.03.216).
Come and say hello at the poster sessions! We've got much to showcase on AI for identification and metadata, PTMs & proteoforms, immunopeptidomics, benchmarking, and open resources. From Monday to Wednesday, CompOmics is present(ing).
#HUPO2025 #Proteomics #MassSpec
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CompOmics activities at HUPO (slide with portraits and titles). Keynote: Lennart Martens — ‘The striking power of diversity: AI models to valorize large-scale proteomics data’ (Mon morning, OS02.01, Harbour AB). Oral abstracts: Tine Claeys — ‘MLmarker: ML framework for tissue-of-origin inference and biomarker discovery’ (Tue afternoon, OS21.02, Harbour AB); Tim Van Den Bossche — ‘Improving metaproteomics data analysis with the Ghent Metaproteomics Toolbox’ (Mon afternoon, OS12.02, Pier 4–5); Ralf Gabriels — ‘MS²DIP: Embracing PTMs for spectrum prediction with graph neural networks’ (Wed afternoon, OS30.02, Pier 4–5). 3-Minute Thesis: Alireza Nameni — ‘The overambitious chef: Balancing model complexity and reliability in proteomics data’ (Mon morning, OS11.7, Harbour C). Pre-congress training: Tine Claeys — ‘What AI in Proteomics Really Needs: Metadata That Works’ (Sun morning, PTC01.01, Harbour C). Thursday ECR session: Pathmanaban Ramasamy — ‘Innovative Approaches to Study Protein Function’ (Thu morning, ECR.01, Pier 4–5). Bioinformatics Hub: ‘Is our proteomics data ready for AI?’ (Claeys, Gabriels, Wein; Tue morning, BI03, Pier 2–3); ‘mzPeak: scalable, interoperable MS format’ (Van Den Bossche with Wein & Kohlbacher; Tue morning, BI05, Pier 2–3); ‘ProteoBench: community platform for workflow comparison’ (Devreese, Bouwmeester, Jachman, van Puyenbroeck with Perez-Riverol & Panse; Wed afternoon, BI07, Pier 2–3).
Getting ready for a busy and exciting #HUPO2025 in Toronto! We’ll present on AI-driven peptide identification, tissue deconvolution, metaproteomics, and more. Join the #bioinformatics hub sessions on ProteoBench, mzPeak, and PSI-AI—community input welcome!
#Proteomics #MassSpec
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Our latest paper introduces new methods for improving peptide retention time predictions in proteomics, incorporating chemical structure information to better handle unseen modifications.
Read all about it in our preprint by👉 doi.org/10.1101/2025...
#Proteomics #AI #MachineLearning
Join us for the EuBIC-MS Winter School 2026! This conference comes highly recommended—excellent keynotes, hands-on workshops, and a very welcoming community.
Arthur Declercq, who just completed his PhD in our group, will deliver a keynote on #immunopeptidomics and #neoepitope prediction.
MLMarker is live! This ML-tool predicts tissue similarity and uncovers biomarkers from your proteomics data. It was trained on public data of healthy human tissues.
Preprint & app: www.biorxiv.org/content/10.1...
Let's chat at #EuPA2025 - Award session (Wednesday) & poster session (Thursday)!
Plenary talk Lennart Martens Rise of the Robots – definitely artificial, somewhat intelligent Keynote lecture Tim Van Den Bossche Improving metaproteomics data analysis with the Ghent Metaproteomics Toolbox Oral presentations Harikrishnan Ramadasan Bridging expert curation and LLMs for automated metadata extraction in lesSDRF 2.0 Robbe Devreese Collisional cross-section prediction for peptides and small molecules: covering all bases (and bridging the gap?) Robbin Bouwmeester Challenges and opportunities in modification searches for DIA proteomics Educational session Lennart Martens No more surprises: AI predictions in MS DDA and DIA data interpretation Robbin Bouwmeester A deep dive into limitations of modification searching for DIA data Caroline Jachmann Fantastic PTMs and how (not?) to find them using msqrob2PTM - a real-life journey Poster presentations Enrico Massignani Overcoming challenges in non-canonical protein searches with OpenProt and ionbot Pathmanaban Ramasamy Assessing the relation between protein phosphorylation, AlphaFold3 models and conformational variability Toon Callens Advancing tissue prediction using read-based DNA methylation modelling towards a multi-omics integration Tine Claeys MLMarker: Data-driven discovery of tissue similarity and biomarkers Alireza Nameni Enhancing peptide-spectrum match identification with non-linear models in Mokapot: Assessing complexity, overfitting, and false discovery rates Tim Van Den Bossche The Metaproteomics Initiative: An international community by and for metaproteomics researchers Award presentations Tine Claeys Bioinformatics Award Tim Van Den Bossche Vision & Commitment Award
From PTMs to proteins, from metadata to metaproteomics. CompOmics has got you covered at #EuPA2025!
We are working on an AI based metadata extraction pipeline from papers, supplementary files and mass spectra. Come to @harirmds.bsky.social's talk at #EuPA2025 for the newest and hottest results!
An older posts I meant to share, but @matrixscience.bsky.social had a really fun write-up on the significant benefits you get by mixing in a little @compomics.com to your workflow (MS2PIP via @ralf.gabriels.dev et al.).
www.matrixscience.com/blog/using-m...
Got a brilliant keynote speaker in mind? We're collecting suggestions for the EuBIC‐MS Winter School 2026 in the Czech Republic next January. Share your ideas now: forms.gle/6Y1ibMuezEB1...
#EuBIC2026 #TeamMassSpec #ProteomicsSky
🚀 New preprint alert! We've improved IM2Deep for accurate peptide collisional cross-section (CCS) prediction, even for peptides exhibiting multiple conformations in the gas phase! 🎯
Check it out here:
www.biorxiv.org/content/10.1...
Seems reasonable to dedicate my first Bluesky post to the following:
Our latest research, TIMS²Rescore, is now published in Journal of Proteome Research! 🎉
Read it here: pubs.acs.org/doi/full/10....
A huge thanks to all our collaborators for making this happen!
Do you want to explore the PTMs you identified in your last MS experiment in a fun, interactive way? Try it out on our PTMVision web server at ptmvision-tuevis.cs.uni-tuebingen.de and check out the new publication in JPR at doi.org/10.1021/acs....!
🚨 Big news, #TeamMassSpec! 🚨
How do we unlock proteomics data reuse, tackle metadata challenges, and harness public (clinical) data for AI?
Find out at HUPO-PSI Spring Meeting 2025!
📅 March 31 – April 3, 2025
📍 Tübingen, Germany
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Recently, We saw a discussion on the role of open-source in proteomics. Here, experienced developers & researchers maintaining OS tools for years shared this comment to guide newcomers in the field about OS and its role in the field. 💻 #Proteomics #OpenSource chemrxiv.org/engage/chemr...
Caroline Jachmann presenting her work in front of the BePAc 2024 audience
Robbe Devreese presenting his work at BePAc 2024
Today, @robbedevr.bsky.social and @carojachmann.bsky.social presented their work on #IM2Deep and #ProteoBench at #BePAc2024.
Learn more at doi.org/10.1101/2024... and proteobench.readthedocs.io.
@pathmanaban.bsky.social featuring #EuPA's Young Proteomics Investigators Club at #BePAc24
