Tine Claeys
Postdoc in computational proteomics @CompOmics @VIBLifeSciences - turning public data into tissue biomarkers with ML, AI, and a mission to make proteomics truly reusable
- Work of my first PhD student, Sam, who fully stumbled down the de novo rabbithole!
- 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
- 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
- Reposted by Tine Claeys🚀 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
- 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.
- 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.
- Reposted by Tine ClaeysReally 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
- Reposted by Tine Claeys🚨 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
- 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)!
- And you get the cutest mascotte octopus. His name is Mark! He'll guide you Clippy-wise through your analyses 🙌
- Reposted by Tine ClaeysFrom 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!
- Join us in Saint-Malo for the #EuBIC-MS session at #EuPA2025! After a short introduction, we have three exciting talks lined up, as well as an interactive discussion on open issues in computational proteomics. @eupaproteomics.bsky.social @uszkoreitju.bsky.social @harirmds.bsky.social
- Reposted by Tine ClaeysNew 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...
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- 🚧 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 🙏
- And please annotate your data with SDRF so we know which file has which sample 🙏
- New to proteomics?? We have like one rule! Make your data available!! proteomicsnews.blogspot.com/2025/04/subm...
- A great first day of the #HUPO PSI meeting about making proteomics #AI ready. Here are some insights! 💡Juan Antonio @pride-ebi.bsky.social first talked about what really is AI-ready data, what is the end goal. (1/5)
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- Reposted by Tine Claeys🚀 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...
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- Reposted by Tine ClaeysSeems 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!
- The @eubic-ms.org Dev Meeting was amazing! We explored how to automatically extract metadata. I'm super excited to continue this effort 🤗 A huge thanks to the incredible team of this hackathon 🙏 #EuBIC2025
- Reposted by Tine ClaeysDo 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....!
- Already 40 people signed up for the HUPO-PSI Spring Meeting! We'll explore the AI-readiness of our proteomics data and need as much input as possible, so register here: www.psidev.info/spring-meeti...
- 🚨 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 (1/4)
- This year’s meeting is all about advancing data reuse and AI applications in proteomics. Whether you're a coding expert, a beginner, or simply passionate about the future of proteomics, there’s something for you! (2/4)
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- Using the BlueSky boost to get some questions finally answered! How many of you report the passage number of your cell lines in your manuscript/metadata annotation? Just wondering how this could impact reproducibility of #proteomics results. #TeamMassSpec
