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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!

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/...

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

Computational #Metaproteomics Preprint out ! MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics Kai Cheng, Daniel Figeys bioRxiv 2026.06.12.728088; doi: doi.org/10.64898/202...

Tomorrow, the 7th International Metaproteomics Symposium begins! Looking forward to 3.5 days of cutting-edge research, stimulating discussions, and reconnecting with the amazing metaproteomics community. #IMS2026 #Metaproteomics Program here: www.hs-anhalt.de/landingsites...

Preprint Alert! PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics www.biorxiv.org/content/10.6...

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/

The computational framework “Peptonizer2000” improves taxonomic assignment in complex #microbiomes by reducing ambiguity in protein-to-taxon mapping and increasing reliability of community profiling. #Metaproteomics #Proteomics 📄https://doi.org/10.1021/acs.jproteome.5c00567 👤EVBC member: Thilo Muth

Save the Date: Our 22nd YPIC Webinar! 📅 July 1st ⏰ 4:00 PM CEST When an unexpected finding shifts your research, how do you build a fundable proposal? 👉 Registeration: us06web.zoom.us/meeting/regi... #WeAreYPIC #GrantWriting #Proteomics #Webinar

Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accurac...

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust prot...

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...

Metaproteomic peptide identification is constrained by the structure and size of the protein search space. Pooled gene catalogues provide coverage but obscure genome-level evidence, and current workfl...

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.