1/3) New preprint on FDR in DIA and DDA proteomics: “diagFDR: Verifiable FDR Reporting via Scope, Calibration, and Stability Diagnostics”: www.biorxiv.org/content/10.6... It argues that “1% FDR„ is often ambiguous in modern workflows. Question: When you report FDR, what exactly do you mean by it?

Structure-informed deep generation enables de novo metabolite annotation in untargeted metabolomics www.nature.com/articles/s41... #jcampubs

New Article! Differential protein expression analysis of quantitative mass spectrometry data using DEqMS

Take a look at our recent work! Happy to see the results of combining classical structural biology, cell-based work, and integrative modelling using cross-linking mass spectrometry (And I also had the opportunity to experiment with Blender to visualise our science a bit!)👇🏻

Comprehensive and timely Review article: Navigating multi-omic integration methods for human microbiome research. Nat Microbiol (2026). doi.org/10.1038/s415...

Gao, Y., Kim, J., Wu, R. et al. Metaproteomics uncovers the functional capacity of a soil microbiome. Sci Rep (2026). doi.org/10.1038/s415...

Out now in Nature Communications! We show that Dictyostelium vaults associate with ER and NE membranes in situ and encapsulate ribosomes with defined orientations, shining new light on their cellular function! #TeamTomo #TeamMassSpec #ProtistsOnSky www.nature.com/articles/s41...

A new preprint introduces π-MSNet: a billion-scale, MS data portal with 1.66B spectra, built for machine/deep learning, benchmarking, and reproducibility. URL: www.biorxiv.org/content/10.6... Open, living, and community-driven-this is a big step toward accelerating innovation in proteomics 🚀

van der Burgt and Cobbaert, "Next-generation proteomics in medical laboratories: metrologically sound quantitative protein tests vs. innovative and personalized proteome patterns" doi.org/10.1515/cclm...

Clinical proteomics is at a crossroads: Should labs prioritize the precision of mass spectrometry or embrace the speed of high-throughput profiling? ⚖️🤔 www.news-medical.net/news/2026041... #Proteomics #PrecisionMedicine @degruyterbrill.bsky.social

Impressive! The Synthetic Epitope Atlas: High-Throughput Design and Validation of De Novo Antibody-Antigen Complexes Altieri et al. bioRxiv 2026.04.17.719295; doi: doi.org/10.64898/202...

#TeamMassSpec NIST26 is set to be the biggest change since NIST98 - a revolutionary rather evolutionary upgrade for both GC-MS and LC-MS [email protected]

(MS Reviews) Editorial for the Special Honor Issue Honoring Dr. Carlito B. Lebrilla: Mass Spectrometry Reviews, EarlyView. #MassSpectromRev #MassSpecRSS

NovoGlyco: mapping protein glycosylation in prokaryotes Martin Pabst, Dinko Soic bioRxiv 2026.04.15.718822; doi: doi.org/10.64898/202...

Excited to share our new @natcomms.nature.com study with the @garyrlewin.bsky.social lab and @amapruns.bsky.social. Using deep visual proteomics, we created the first neuronal subset-resolved proteomic map of sensory neurons with potential implications for pain treatment. go.nature.com/481nr4R

MetaDIA: A DDA-free Database Reduction Strategy for DIA Human Gut Metaproteomics url: academic.oup.com/gpb/article/...

Come join us a #bioinformatics / #computationalbiology postdoc to explore the #microbiome using #metaproteomics and #metagenomics Microbiome Bioinformatician (Postdoc) - Metagenomics and Metaproteomics @RalserLab Charité Universitätsmedizin Berlin See the full job description on jobRxiv: https://j

Metabolomics across scales: from single cells to population studies

A study published in Nature presents CHARM, a single-cell 'four-omics' sequencing method that profiles genome conformation, histone modifications, chromatin accessibility, and gene expression within the same cell.🧪👇 www.nature.com/articles/s41...

Review on 20 years of Orbitrap MS! analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/... From early days to today’s hybrid & Tribrid systems, it highlights how innovation, accessibility, and new applications shaped the field. Orbitrap => true workhorse of modern MS 🔬

The #UPSS2026 video has landed! Thank you to all the participants, organizers, sponsors, facilitators and collborators for making this event such a success! Please follow our socials to hear about the launch of #UPSS2027... #LearnConnectGrowExplore with #TeamMassSpec youtu.be/5BvnY-RyqRo

InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics Preprint: doi.org/10.1101/2025...

🚨 The final programme for the Annual Proteomics Gathering at the Faculty of Pharmacy, Universidad Complutense de Madrid on April 16th is officially ready! 🎉 #AnnualProteomicsGathering #Networking #ScienceCommunity #YoungResearchers #InnovationInScience #FlashTalks #EarlyCareerResearchers #YPIC

I thought it was quite mind boggling to see that around 10% of the protein in a standard yeast based bread is actually yeast protein! Here our #metaproteomics analysis of microbial protein in fermented foods pubs.rsc.org/en/Content/A... Congratulations to first authors Laura Winkler and Ayesha Awan

Big fan of this lab’s work! Casanovo is already state-of-the-art for de novo sequencing; and these improvements take it even further: better score interpretability, database search integration, faster runtimes, and user-friendly workflows. pubs.acs.org/doi/10.1021/...

New Preprint: NovoTax identifies the closest prokaryotic genome directly from raw bottom-up proteomics data. The approach combines peptide de novo sequencing tools on DIA data with an optimized implementation of peptide searching through an extensive genome database. www.biorxiv.org/content/10.6...

We evaluated quantification methods for #metaproteomics and found that area under the curve quantification (AUC) outperforms spectral counting. Importantly, using match between runs for AUC quantification results in lots of false detections and should not be used www.biorxiv.org/content/10.6...

ECLIPSE: Exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas www.biorxiv.org/cont... --- #proteomics #prot-preprint

In-source fragmentation in mass spectrometry-based proteomics: prevalence, impact, and strategies for mitigation doi.org/10.64898/202...

"The department needs papers, because papers justify funding, & funding justifies the department. ... Whether that student walks out the door five years later as an independent thinker or a competent prompt engineer is, institutionally speaking, irrelevant." ergosphere.blog/posts/the-ma...

1) Proteomics has a severe problem. We keep pretending database search is “good enough”, while systematically missing everything that isn’t already known. No genome/proteome → no ID Variant peptide → invisible Novel biology → filtered out

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

ReactomeGSA: new features to simplify public data reuse academic.oup.com/bioinformati...

Check out our new paper applying fast DIA proteomics to bacterial co-cultures at scale. www.nature.com/articles/s41... @kiranrpatil.bsky.social

Welcome to the battle against Brucellosis disease: Field isolates proved more resistant than lab strains, req. stricter conditions (95°C or 0.6% formaldehyde). Proteomics reveals why: heat exposes epitopes (“cooking”), formaldehyde preserves structure (“freezing”). journals.plos.org/plosntds/art...

Exited to share our latest work! Out now in @natcomms.nature.com Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA! www.nature.com/articles/s41...

Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks www.biorxiv.org/cont... --- #proteomics #prot-preprint

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches www.biorxiv.org/cont... --- #proteomics #prot-preprint

I 100% agree with this take. Plug: If you are working with #proteomics and/or #massspec data, check out our shortcourse at #ASMS2026 to get a jump start on many of these methods! (Course 04 here: www.asms.org/conferences/...)

New MS2DeepScore release (2.9.0) 🚀 --> github.com/matchms/ms2d... The main change is the ability to use count and log-count rdkit fingerprints, as well as unfolded fingerprints for training. #opensource #massspec #Python

Steve Brunton‘s YouTube Channel on statistics and machine learning - what a fantastic ressource for students and life-long learners: www.youtube.com/@Eigensteve #OpenScience #Statistics #MachineLearning #Learning

Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics | Microbiology Spectrum journals.asm.org/doi/10.1128/...

Great perspective article published in JPR comparing classic vs. ML-based peptide identification search in proteomics: Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

Excited to share our new Prosit-PTM paper is out! A deep learning model that predicts MS2 spectra and Retention time for modified peptides, using chemically informed encodings and data augmentation based on amino acid substitution to learn general rules for how PTMs affect spectra.

Do you find it difficult to understand why LLMs — like ChatGPT and the like — are a form of ‘automated plagiarism’? Take 3 min and listen to this excellent explanation by @gwenvarley.bsky.social youtu.be/1ON-FJHq9aM?... (h/t @olivia.science) 1/🧵

Halfmarathon. Finished an unoptimized experiment on endurance today. It was much fun, fatique and suffering. 😉 Keep on running… 🏃‍♂️

Published in NAR: expanded reference catalog of translated open reading frames for biomedical research academic.oup.com/nar/article/...

Our article has been published today in @PeerJSTM peerj.com/articles/20990 #Bioinformatics #EcosystemScience #Microbiology #Oncology

AI redefine untargeted metabolomics: estimating chemical amounts for a Human Exposome Project www.frontiersin.org/journals/pub...

Fermented foods aren’t just transformed by microbes, they also contain them. Using metaproteomics for 17 foods, Winkler et al. show microbial proteins make up to 11% of total protein and 60% of identified diversity, with potential impacts on gut function and health. 🧫🥬 pubs.rsc.org/en/content/a...