Ralf Gabriels

Unlocking the Next Decade of Proteomics with Standardized, Structured Metadata The proteomics community has fully embraced data sharing, yet data set metadata provision remains limited, especially at the level of the biological samples and experimental design. This hampers large...

This proteomics banger from @compomics.com and @ebi.embl.org folks looks great. It is one of those titles that makes some people really excited and others let out an audible groan (I’m in the former).

pubs.acs.org/doi/full/10....

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

🧵 ½

I do realize that as one of the organizers, I might be somewhat biased here. But that being said, there's a good reason I joined the organizational team directly after my first EuBIC-MS event 😁

These events have always been the highlight of my academic year. Want to connect to the computational mass spec community in Europe and beyond in a highly positive and welcoming environment? Join this conference!

Conference stage with Marie Locard-Paulet, the chairs, and the opening slide in the background.

Marie Locard-Paulet presenting the EuBIC-MS #ProteoBench project at the #EuPA2025 conference.

👉 Learn more about our open proteomics software benchmarking platform at proteobench.readthedocs.io.

#Proteomics #Bioinformatics #Benchmarking

I don't think that they are. @eupaproteomics.bsky.social?

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

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!

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...

MS2Rescore found its way into #ProteomeDiscoverer 🥳 At least, somewhat, through #MascotServer. Thanks for the implementation and for the nice blog post, @matrixscience.bsky.social!

www.matrixscience.com/blog/using-m...

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...

🚀 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...

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.

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!

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

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
(1/4)

ProHap - Search your proteomics data against population variants! Critically important new community resource! STOP. IGNORE THE FLOWCHART ABOVE. These are bioinformatics people, they think this stuff is mandatory. I assume their conferences all have...

This new resource is AMAZING. You can easily search (re-search) your proteomics data in the context of human genomics (you know, that whole thing where we don't all have the exact same genome?) Read the paper, but instructions in the blog post - proteomicsnews.blogspot.com/2024/12/proh...

Open-source and FAIR Research Software for Proteomics Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and in...

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...

Hi #TeamMassSpec! #FeMS+ has joined BlueSky! Please share and get the word out so we can build up a base here.

In that case, Italian should get you there most of the way 😄

I do believe mostly German is spoken in Brixen, although they are officially bilingual.

In any case, super glad you'll be there!

Happy to announce MS²Rescore v3.0, our much-improved platform for #MachineLearning driven rescoring of #Proteomics search results.

A big thanks to Louise Buur and Viktoria Dorfer for the great collaboration!

Open access full text: biblio.ugent.be/publication/...
Project: github.com/compomics/ms...

The state of vendor market share in bottom-up proteomics - a tale from published ProteomeXchange datasets.

1. Bruker has the greatest momentum with a 4-fold increase since 2017
- timsTOFs are largely responsible for this increase

2. Sciex is gradually losing market share

Super happy to see MS²PIP spectrum predictions implemented on the ProteomeXchange USI lookup service!
proteomecentral.proteomexchange.org/usi/?usi=mzs...

Have you ever noticed how benchmarking #proteomics data analysis can be a wild west?

EuBIC-MS community members did, and started #ProteoBench: An open platform for comparing proteomics data analysis workflows.

Learn more at the webinar (27 Feb, 18h CET) Register here: bit.ly/3SfS4Lf

I think it was Robbin Bouwmeester’s talk at EuBIC where it was SAGE to MS2Rescore and it seemed quietly bad ass. This update is making it look even more attractive as my new fav proteomics pipeline.

Very surprised to see this published without any external FDR control testing...

Thomas Burger presents remotely at the EuBIC-MS Winter School 2024

Cecilia Lindskog presenting at the EuBIC-MS Winter School 2024

Ben Neely presenting at the EuBIC-MS Winter School 2024

After the educational day with hands-on tutorials, day 2 of the #EuBIC2024 Winter School started with great keynotes by Thomas Burger, Cecilia Lindskog, and @benneely.com.

I was hoping people registering would have as much fun with it as me when setting up the form 😅

Not sure how much of EuBIC is actually on Bluesky, but @magnuspalmblad.bsky.social has a feed for the conference to capture the hashtag. Get it!

EuBIC Winter School 2024 Five days of keynotes, workshops, flash talks, posters, and more on computational mass spectrometry 15-19 January 2024 @ Winterberg, Germany https://www.eubic-ms.org/events/2024-winter-school Keynote speakers: Ben Neely, Cecilia Lindskog, Dirk Valkenborg, Juan Antonio Vizcaino, Laurent Gatto, Nils Hoffmann, Niveda Sundararaman, Robbin Bouwmeester, Thomas Burger, Wen-Feng Zeng Special guest: Ben Orsburn Sponsors: MSAID, Evosep, Matrix Science, Bioinformatics Solutions Inc Powered by: EuPA, PROTrEIN, de.NBI

Only four more days for early bird registration for the #EuBIC2024 Winter School ⏲️

Registration info on eubic-ms.org/events/2024-...