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Group Leader & Adjunct Prof 🧑‍🏫 | Building scalable, FAIR data platforms for public health epidemiology | Bioinformatics & mass spectrometry 📈 | Based in Berlin | Open science & real-world impact 🔬✨

Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021–2025) | Analytical Chemistry pubs.acs.org/doi/10.1021/...

Reshaping of the fecal proteome and metaproteome in obese patients 2 years after bariatric surgery | mSystems journals.asm.org/doi/10.1128/...

Another hidden gem by Gelio Alves and co-workers: Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation–Maximization Approach | Journal of the American Society for Mass Spectrometry pubs.acs.org/doi/10.1021/... It is worth to look at Gelio‘s publications!

When it's time to pick the best peptides for targeted MS, Bromo doesn't just guess from sequence. It learns from millions of peptide comparisons, considers charge, and ranks precursors by their response. And it adapts faster than a bromance at a #ASMS coffee break! www.biorxiv.org/content/10.6...

New preprint on the current bottlenecks of deep learning-based methods for de novo peptide sequencing that underuse physical properties of spectra and how to overcome this with MemNovo: arxiv.org/abs/2606.11868

Early use of directed acyclic graphs to speed up analysis of mass spectrometry of peptides. Low polynomial time complexity, down from exponential complexity without DAGs. en.wikipedia.org/wiki/De_novo... doi.org/10.1002/bms.... #DAG #Peptide #sequencing

scpviz: A Python bioinformatics toolkit for Single-cell Proteomics and multi-omics analysis joss.theoj.org/paper... --- #proteomics #prot-paper

Mass spectrometry proteomics loves benchmarks. But an important one is rare: - Accuracy of proteome quantification when using short LC gradients. Fast MS instruments can quantify 7 - 9k proteins from 200ng samples using short separation times affording the analysis of 200 – 500 samples / day. 1/

Abstract submission and registration for the Proteomic Forum / EuPA 2026 are still open. Submit your abstract, secure your spot, and join the proteomics community in Würzburg. 📝 Abstract deadline: 30 June 2026 🎟 Early bird deadline: 15 July 2026 👉 Everything in one place: proteomic-forum.com

This banger from Matt @mattwfoster.bsky.social et al. just dropped. Love some whole blood proteomics fun, and really so much of what Matt has been doing with blood. Excellent work! pubs.acs.org/doi/10.1021/...

De novo peptide sequencing from tandem mass spectrometry is pivotal in proteomics, enabling identification of novel peptides without reference databases. While recent Transformer-based encoder-decoder...

It is increasingly recognized that the ‘omic analysis of whole blood has applications for precision medicine and disease phenotyping. Despite this realization, whole blood is generally viewed as a challenging analytical matrix in comparison to plasma or serum. Moreover, proteomic analyses of whole blood have almost exclusively focused on (non)targeted analyses of protein abundances and much less on post-translational modifications (PTMs). Here, we developed a streamlined workflow for processing 20 microliters of venous blood collected by volumetric absorptive microsampling that incorporates serial trypsinization and N-glycopeptide and phosphopeptide enrichment and avoids laborious sample dry-down or cleanup steps. As many as 10,000 analytes (reported as protein groups, glycopeptidoforms, and phosphosites) can be quantified by liquid chromatography-tandem mass spectrometry in under 2 h of MS acquisition time. Using these methods, we explored the stability of “dried” and “wet” blood proteomes, as well as the effects of ex vivo inflammatory stimulus or phosphatase inhibition. Multiomics factor analysis enabled facile identification of analytes that contributed to interindividual variability of the blood proteomes, including N-glycopeptides that distinguish immunoglobulin heavy constant alpha 2 allotypes. Collectively, our results help to establish feasibility and best practices for the integrated MS-based quantification of proteins and PTMs from dried blood.

Metabolomics software development has accelerated rapidly, yet no recent systematic analysis has quantified how the landscape is evolving across computational methods, geographies, and the research co...

Bariatric surgery is widely recognized as the most effective and durable intervention for severe obesity; however, its long-term molecular effects on gut microbiota-host interactions remain poorly understood. By applying shotgun metaproteomics to fecal samples collected before and 2 years after surgery, our study provides novel insights into the functional consequences of bariatric bypass procedures. We demonstrate sustained alterations in both microbial and host protein profiles, including metabolic enzymes, outer membrane proteins, and immune-related factors, revealing a long-lasting remodeling of gut ecosystem functions. These findings underscore the value of metaproteomics in uncovering molecular mechanisms underlying bariatric surgery outcomes and may ultimately guide the development of microbiome- or host-targeted strategies to optimize therapy and long-term patient care.