@robbinbouwmeester.bsky.social and @robbedevr.bsky.social are amongst those presenting at the latest EuBIC-MS seminar held in context of the yearly ProteoBench hackathon in Copenhagen, Denmark. Hope to see you there!

EuBIC-MS@eubic-ms.org · 5mo ago

On the 15th of April we will host a seminar as part of our ProteoBench hackathon in Copenhagen. Swing by and hear more about Protebench, EuBIC and other interesting projects! Find details here: eubic-ms.org/events/lates... See you there! 😄

📢 Mark your calendars! We’re excited to announce the EuBIC-MS 2027 Hackathon! 📍 Gimo, Sweden 📅 31 January – 5 February 2027 💡 Have a hackathon idea? The call for topic proposals is now open on the EuBIC GitHub repository: github.com/EuBIC/EuBIC2... We’re looking forward to seeing you there!

GitHub - EuBIC/EuBIC2027: Organizational repository for the EuBIC-MS Hackathon 2027

Organizational repository for the EuBIC-MS Hackathon 2027 - EuBIC/EuBIC2027

github.com

Happy to have this one finally out. Since the first generation was very popular in the proteomics community, we decided to work on a second generation including the latest innovations in LC-MS. Very grateful to all collaborators and a special shoutout to @robbedevr.bsky.social from @compomics.com

PastelBio@pastelbio.bsky.social · 7mo ago

LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients www.biorxiv.org/cont... --- #proteomics #prot-preprint

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

Our latest paper introduces new methods for improving peptide retention time predictions in proteomics, incorporating chemical structure information to better handle unseen modifications. Read all about it in our preprint by👉 doi.org/10.1101/2025... #Proteomics #AI #MachineLearning

iDeepLC: chemical structure information yields improved retention time prediction of peptides with unseen modifications

Deep learning has notably advanced the field of liquid chromatography–mass spectrometry-based proteomics. Accurate prediction of peptide retention times significantly enhances our ability to match LC-...

doi.org

Join us for the EuBIC-MS Winter School 2026! This conference comes highly recommended—excellent keynotes, hands-on workshops, and a very welcoming community. Arthur Declercq, who just completed his PhD in our group, will deliver a keynote on #immunopeptidomics and #neoepitope prediction.

EuBIC-MS@eubic-ms.org · 10mo ago

Registration is now open for the EuBIC-MS Winter School 2026! Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS. Info and registration: eubic-ms.org/events/2026-... #EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics

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)!

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!

EuBIC-MS@eubic-ms.org · last yr.

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

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...

Got a brilliant keynote speaker in mind? We're collecting suggestions for the EuBIC‐MS Winter School 2026 in the Czech Republic next January. Share your ideas now: forms.gle/6Y1ibMuezEB1... #EuBIC2026 #TeamMassSpec #ProteomicsSky

Keynote speaker nominations for the EuBIC-MS Winter School 2026

Hello and welcome! This form is your opportunity to nominate a keynote speaker for the EuBIC-MS Winter School 2026. If you have a standout suggestion, please complete the form thoroughly and thoughtf...

forms.gle

🚀 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...

biorxiv.org

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

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)

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...

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...

chemrxiv.org

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.

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