Tine Claeys

Work of my first PhD student, Sam, who fully stumbled down the de novo rabbithole!

Check our website: psi-ai.org
Looking forward to where this will take us!
A huge thanks to all attendees and of course to my co-chairs Samuel Wein and @ralf.gabriels.dev

Aug14_Kickoff.mp4 Managed Nextcloud - powered by hosting.de

The AI-working group of the Proteomics Standards Initiative officially launched! #AI is increasingly present within #proteomics, we want to support the community to get the most out of their data and models. For this, we need your input #TeamMassSpec
Rewatch the kickoff event: tinyurl.com/37cz9bnj

Metadata from the paper is often too incomplete to reuse the dataset without extra tools, even raw file species mapping is a disaster! Authors need better reporting guidelines so at least the paper is complete, or they need to make an SDRF (preferably both).

I fully agree as well, that is the endgoal! That would however require then also treating it as pub with (i) enforcable metadata and peerreview/validation; (ii) doi for citations; (iii) impact metrics for grants.
Maybe the rise of clinical datasets might push this?

repository.jpostdb.org/entry/JPST00...

Authors need to inform repositories that their paper got published, right? PRIDE has built-in automatic checks in case the authors would forget. Having a bunch of public datasets that don't link back to a paper is also not ideal. Unless there is proper metadata I'd suppose?

Never know that there were so many ''condoms'' involved in studying open reading frames, the more you know 🤷‍♀️

Yes, enjoyong the amazing british weather, luckily there's tea 😉 I'm flying back directly after the conference but will keep it in mind for future EBI visits 🤗

Up before sunrise and a little nervous, it’s my first keynote ever!
Speaking tonight at #ISMB2025 in the CompMS track about making proteomics AI ready. Expect metadata, MLMarker, and a lot of public data love. See you there!
@iscb.bsky.social

🚀 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

ProteomicsML is absolutely awesome to get hands-on with the ML learning part and learn the classical pitfalls

Depends on where you want to start in your data process (raw files, PSMs, identifications?)
I'd say that AI-readiness is 75% preprocessing and getting all data in the same format plus scalability of your scripts. There are some good packages like psmutils and pyopenMS but depends on your specifics.

Mark is the cutest octopus which will guide you through #AI driven biomarker identification in your proteomics sample (preprint: www.biorxiv.org/content/10.1...
Pretty clear that @compomics.com is thé best team to do science and have fun with 🙌

Last weeks #EuPA2025 was a blast! From receiving the Bioinformatics Award for my #metadata and community efforts with getting the opportunity to present my work, to building sandcastles in the shape of the logo of my newest tool MLMarker.

Mark is the cutest octopus which will guide you through #AI driven biomarker identification in your proteomics sample (preprint: www.biorxiv.org/content/10.1...
Pretty clear that @compomics.com is thé best team to do science and have fun with 🙌

Last weeks #EuPA2025 was a blast! From receiving the Bioinformatics Award for my #metadata and community efforts with getting the opportunity to present my work, to building sandcastles in the shape of the logo of my newest tool MLMarker.

Really liking @tineclaeys.bsky.social's metaphor on metadata:
It's like the philosopher's stone, turning your experimental data into gold and giving it the elixir of life.

Congrats with the EuPA Bioinformatics Award, Tine!

#EuPA2025

🚨 Has PRIDE helped your research?

Take 15 mins to tell funders why open data matters!
📊 Fill out the EMBL-EBI 2025 survey 👉
www.surveymonkey.com/r/QGFMBH8?ch...

Your feedback helps keep PRIDE open, FAIR & impactful.
🙏 Please share!
#FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE

And you get the cutest mascotte octopus. His name is Mark! He'll guide you Clippy-wise through your analyses 🙌

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!

DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setups While LC retention time prediction of peptides and their modifications has proven useful, widespread adoption and optimal performance are hindered by variations in experimental parameters. These varia...

New in DeepLC! Ability to deal with wild, weird, and wobbly LC setups or peptide modifications. This ability is possible with transfer learning; where only a minimal amount of training peptides are needed for accurate retention time predictions.

www.biorxiv.org/content/10.1...

🎉 Big news from the @pride-ebi.bsky.social Team! 🎉

We’re officially in #ASMS2025 mode and kicking things off with a major milestone:

🚀 Introducing PRIDE-AP – the first Affinity Proteomics archive!
🔗 www.ebi.ac.uk/pride/archiv...

A new home for your #Olink and #SomaScan and other non-MS data.👇

What an amazing ride these past 2 years with @ypic.bsky.social! So proud of what we have built together.

Now it is your turn! And it is such a great opportunity to support #ECRs and grow with the #proteomics community 🥰

Highly recommend applying! 🙌

Wondering about the next step in your proteomics career? Curious to know how proteomics experts ended up at their current positions? Looking for tips to help you discover what you really like? Join our Meet-the-Expert session! Wednesday, June 18th | 12:30 - 13:30 Vauban 2 #EuPA2025 #EuPAFPS2025

What’s new:
Fewer clicks, smoother annotation, ontology browsing and community suggested terms for single-cell proteomics, immunopeptidomics, etc.

🚧 Refactored lesSDRF; feedback welcome!

I’ve pushed a new version of lesSDRF to make high-throughput SDRF annotation faster and more intuitive.

Github issue: github.com/CompOmics/le...
Temporary app: refactorlessdrf.streamlit.app

I could use some feedback before making this the new lesSDRF 🙏

No clear guide exists, sounds like sth we should provide!
For accession: PRIDE has a good API but different file formats can require tremendous conversions and parsing.
For submitting: lesSDRF supports up to 500 files. The team from PRIDE has amazing support so I'd contact @ypriverol.bsky.social 🙌