Tine Claeys
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tineclaeys.bsky.social
Tine Claeys
@tineclaeys.bsky.social
680 followers 270 following 51 posts
Postdoc in computational proteomics @CompOmics @VIBLifeSciences - turning public data into tissue biomarkers with ML, AI, and a mission to make proteomics truly reusable
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tineclaeys.bsky.social
Work of my first PhD student, Sam, who fully stumbled down the de novo rabbithole!
samvpy.bsky.social samvpy.bsky.social @samvpy.bsky.social · Aug 27
Exciting news: Preprint on the limitations of current de novo peptide sequencing models on dealing with sequence ambiguity is now out! It focuses on how current models deal with sequence ambiguity, and when and where they go wrong.

Check it out here: www.biorxiv.org/content/10.1...
Limitations of de novo sequencing in resolving sequence ambiguity
De novo peptide sequencing enables peptide identification from fragmentation spectra without relying on sequence databases. However, incomplete spectra create ambiguity, making unambiguous identificat...
www.biorxiv.org
August 27, 2025 at 8:37 AM
tineclaeys.bsky.social
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
Aug14_Kickoff.mp4
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cloud.samwein.com
August 15, 2025 at 10:48 AM
tineclaeys.bsky.social
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
July 22, 2025 at 5:25 AM
Reposted by Tine Claeys
ypriverol.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
July 11, 2025 at 8:43 AM
tineclaeys.bsky.social
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.
June 23, 2025 at 8:03 PM
tineclaeys.bsky.social
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.
June 23, 2025 at 8:01 PM
Reposted by Tine Claeys
ralf.gabriels.dev
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
June 18, 2025 at 3:06 PM
Reposted by Tine Claeys
ypriverol.bsky.social
🚨 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
LinkedIn
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lnkd.in
June 18, 2025 at 6:02 AM
tineclaeys.bsky.social
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)!
www.biorxiv.org
June 16, 2025 at 9:31 AM
Reposted by Tine Claeys
compomics.com
From PTMs to proteins, from metadata to metaproteomics. CompOmics has got you covered at #EuPA2025!
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
June 16, 2025 at 8:05 AM
tineclaeys.bsky.social
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!
eubic-ms.org EuBIC-MS @eubic-ms.org · Jun 13
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
EuBIC-MS session at EuPA 2025 Tuesday June 17, 10:15 - 12:00, Room Vauban 1 Ralf Gabriels Introducing EuBIC-MS 10:15 - 10:30 Julian Uszkoreit O85 - What can we gain - a comparison of common search engines and post-processing methods 10:30 - 10:45 Yannic Chen O84 - Benchmarking Database Search Engines for DDA-based Immunopeptidomics 10:45 - 11:00 Harikrishnan Ramadasan O86 - Bridging expert curation and LLMs for automated metadata extraction in lesSDRF 2.0 11:00 - 11:15 Interactive discussions on open challenges in computational proteomics 11:15 - 12:00
June 13, 2025 at 9:47 PM
Reposted by Tine Claeys
robbinbouwmeester.bsky.social
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...
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...
www.biorxiv.org
June 4, 2025 at 11:16 AM
Reposted by Tine Claeys
ypriverol.bsky.social
🎉 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.👇
PRIDE - PRoteomics IDEntifications Database
EMBL-EBI
www.ebi.ac.uk
June 4, 2025 at 1:45 PM
Reposted by Tine Claeys
maurinefucito.bsky.social
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! 🙌
ypic.bsky.social ypic.bsky.social @ypic.bsky.social · Jun 3
Text: YPIC Board Elections 2025! Want to be involved in the #proteomics community? 9 roles are open, incl. President, VP, Treasurer & more!
🗓️ Apps open June 4 until July 2
📥 Apply here: forms.gle/t5jhWCmtxWUX...
📢 Be the change in science leadership!
#ScientificLeadership #BoardElections
June 3, 2025 at 7:58 AM
Reposted by Tine Claeys
ypic.bsky.social
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
May 29, 2025 at 7:51 AM
tineclaeys.bsky.social
🚧 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 🙏
May 20, 2025 at 2:25 PM
tineclaeys.bsky.social
And please annotate your data with SDRF so we know which file has which sample 🙏
April 30, 2025 at 2:22 PM
tineclaeys.bsky.social
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)
March 31, 2025 at 2:24 PM
Reposted by Tine Claeys
ypriverol.bsky.social
🚀 Big news! We've just published the official guidelines for submitting affinity proteomics data to PRIDE @pride-ebi.bsky.social (supported technologies Olink & SomaScan)!
Get ahead of the curve—check them out & start your submissions! 👇
🔗 github.com/PRIDE-Archiv...
#Proteomics #Olink #SomaScan
github.com
March 28, 2025 at 7:20 AM
Reposted by Tine Claeys
robbedevr.bsky.social
🚀 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...
Collisional cross-section prediction for multiconformational peptide ions with IM2Deep
Peptide collisional cross-section (CCS) prediction is complicated by the tendency of peptide ions to exhibit multiple conformations in the gas phase. This adds further complexity to downstream analysi...
www.biorxiv.org
February 23, 2025 at 1:12 PM
Reposted by Tine Claeys
magnuspalmblad.bsky.social
Wonderful and productive @eubic-ms.org Developers' Meeting in Neustift, South Tyrol, hacking proteomics and metabolomics software and metadata standards for five days!
February 10, 2025 at 9:56 AM
Reposted by Tine Claeys
robbedevr.bsky.social
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!
TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore
The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields, including plasma proteomics, immunopeptidomics, and metaproteomics, must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments. Technical advancements in MS instrumentation can mitigate these issues by acquiring more discerning information at higher sensitivity levels. This is exemplified by the incorporation of ion mobility and parallel accumulation and serial fragmentation (PASEF) technologies in timsTOF instruments. In addition, AI-based bioinformatics solutions can help overcome ambiguity issues by integrating more data into the identification workflow. Here, we introduce TIMS2Rescore, a data-driven rescoring workflow optimized for DDA-PASEF data from timsTOF instruments. This platform includes new timsTOF MS2PIP spectrum prediction models and IM2Deep, a new deep learning-based peptide ion mobility predictor. Furthermore, to fully streamline data throughput, TIMS2Rescore directly accepts Bruker raw mass spectrometry data and search results from ProteoScape and many other search engines, including Sage and PEAKS. We showcase TIMS2Rescore performance on plasma proteomics, immunopeptidomics (HLA class I and II), and metaproteomics data sets. TIMS2Rescore is open-source and freely available at https://github.com/compomics/tims2rescore.
pubs.acs.org
February 7, 2025 at 2:13 PM
tineclaeys.bsky.social
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
February 7, 2025 at 10:22 AM
Reposted by Tine Claeys
carojachmann.bsky.social
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....!
PTMVision
PTMVision: Interactive Visualization of Post Translational Modifications | Understanding the intricate landscape of post-translational modifications (PTMs) is crucial for unraveling the co...
ptmvision-tuevis.cs.uni-tuebingen.de
January 21, 2025 at 4:02 PM
tineclaeys.bsky.social
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...
HUPO-PSI Spring Meeting 2025 - HUPO Proteomics Standards Initiative
About The HUPO-PSI Spring Meeting is an annual event organized by the HUPO Proteomics Standards Initiative, aiming to advance data standardization efforts. This meeting brings together scientists from...
www.psidev.info
January 20, 2025 at 5:04 PM