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CompOmics

@compomics.com

The CompOmics group specializes in the management, analysis and integration of high-throughput biological data #ResearchGroup #GhentUniversity #VIBLifeSciences

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CompOmics @compomics.com · 09/11/2025

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 🧵 2/2

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).

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CompOmics @compomics.com · 09/11/2025

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

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).

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CompOmics @compomics.com · 16/06/2025

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

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CompOmics @compomics.com · 06/12/2024

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.

Caroline Jachmann presenting her work in front of the BePAc 2024 audience

Robbe Devreese presenting his work at BePAc 2024

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CompOmics @compomics.com · 05/12/2024

@pathmanaban.bsky.social featuring #EuPA's Young Proteomics Investigators Club at #BePAc24

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