Daniel Petras

We are super thankful to everyone who contributed to this massive team effort, and especially Jeff Hawkes, Carsten Simon, Bruno Brandao da Costa, and Jarmo-Charles Kalinski for coordinating and spearheading the study and paper.

The very positive aspect from my perspective: This work highlights the power of open science and large-scale collaboration to move non-targeted metabolomics forward.

There is still room for improvement on data alignment side, and we as community should put more emphasis on method standardization, especially if long-term data comparability and reuse is desired.

Remaining challenges are: That low-intensity signals in DOM showed higher variability, especially for DDA-based MS/MS acquisition. Not so surprisingly, differences in instrument acquisition rates and standardization strongly influence comparability.

The good news is: Data from similar MS platforms with harmonized parameters reveal consistent chemical trends, and high-intensity features, and multivariate analysis aligned well across labs.

This project brought together 50+ co-authors from 24 laboratories, all analyzing identical DOM samples using standardized LC and MS/MS settings. The goal was to check if we all find the same molecules and chemical trends, and to assess how well we can co-analyze data from different labs.

I am super excited that our paper on inter-laboratory comparability of non-targeted LC–MS/MS analysis of dissolved organic matter was just published in ES&T.

pubs.acs.org/doi/10.1021/...

Mapping of the viral shunt across widespread coccolithophore blooms using metabolic biomarkers | PNAS The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon fixed through photosynthesis during algal bloom events ...

🌊Paper announcement! 📣
Viral infections rewire the metabolic makeup of their host and thereby create distinct chemical signatures. Can we use metabolic biomarkers to diagnose infections of algal blooms in the ocean?
Well, take a look at our new article led by Conny Kuhlisch in @pnas.org
>>

let's get the community rolling 💪! Thanks to Vilhelm Suksi from @antagomir.bsky.social 's group for the contribution of the notame vignette 🙌

Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialogue and adaptive strategies with the fungus Botrytis Abstract. Bacterial–fungal interactions have traditionally been attributed to secondary metabolites, but the role of the bacterial extracellular matrix in

Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialogue and adaptive strategies with the fungus Botrytis

#ISMEJournal by @aliciaperezlorente.bsky.social et al from @diegromero.bsky.social and @daniel-petras.bsky.social

academic.oup.com/ismej/advanc...

xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing data set scale and complexity demand adaptable, robust, and reproducible software solutions. Modern preprocessing tools must evolve to integrate seamlessly with downstream analysis platforms, ensuring efficient and streamlined workflows. Since its introduction in 2005, the xcms R package has become one of the most widely used tools for LC-MS data preprocessing. Developed through an open-source, community-driven approach, xcms maintains long-term stability while continuously expanding its capabilities and accessibility. We present recent advancements that position xcms as a central component of a modular and interoperable software ecosystem for metabolomics data analysis. Key improvements include enhanced scalability, enabling the processing of large-scale experiments with thousands of samples on standard computing hardware. These developments empower users to build comprehensive, customizable, and reproducible workflows tailored to diverse experimental designs and analytical needs. An expanding collection of tutorials, documentation, and teaching materials further supports both new and experienced users in leveraging broader R and Bioconductor ecosystems. These resources facilitate the integration of statistical modeling, visualization tools, and domain-specific packages, extending the reach and impact of xcms workflows. Together, these enhancements solidify xcms as a cornerstone of modern metabolomics research.

Out now! xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem doi.org/10.1021/acs....
with Phillipine and @jorainer.bsky.social (EURAC), @metabomichael.bsky.social, Hendrik and Norman from @ipbhalle.bsky.social, @janstanstrup.bsky.social, et al.

Discovery and Heterologous Expression of the Soil Metagenome-Derived Lasso Peptide Metanodin with an Unprecedented Ring Structure Culture-independent metagenomic approaches have proven to be effective tools for identifying previously hidden biosynthetic gene clusters (BGCs) encoding novel natural products with potential medical relevance. However, producing these compounds remains challenging as metagenomic BGCs often originate from organisms phylogenetically distant from available heterologous hosts. Lasso peptides, a subclass of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, exhibit diverse bioactivities, yet no lasso peptide has previously been discovered directly from a metagenome. Here, we report the discovery and heterologous expression of the first soil metagenome-derived lasso peptide. Expression of its biosynthetic gene cluster in Escherichia coli, followed by mass spectrometry analysis, strongly supported the predicted amino acid sequence and lasso structure of the peptide. Notably, this lasso peptide is the first to feature asparagine as the ring-forming residue at position one. Taxonomic analysis of the corresponding BGC identified an uncultivated member of the Steroidobacterales family (Gammaproteobacteria) as the closest known relative of the potential native host. These findings underscore the potential of metagenomic genome mining to reveal structurally novel RiPPs and to expand our understanding of the natural diversity of lasso peptides.

Happy to share our newest manuscript about the discovery and hererologous expression of metanodin, a new lassopeptide with unprecedented structural features directly from soil metagenomes. pubs.acs.org/doi/full/10....
#secmet #lassopeptides #syntheticbiology

We are super excited that our new paper on microfluidic-based LC-MS/MS fractionation in combination with bioluminescence bioreporters readouts, for compound-resolved bioactivity metabolomics, was just published: pubs.acs.org/doi/10.1021/...

What a fun day! Thanks so much for stopping by Pieter!

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes Phylogenetic analysis is widely used to predict enzyme function, yet building annotated and reusable trees is labor-intensive and requires extensive knowledge about the specific enzymes. Existing reso...

Happy to share our newest preprint. PhyloNaP as a user friendly database of phylogeny for enzymes involved in natural product production and as public repository for well curated phylogenetic trees. Happy Tree Building!!!
#phylogeny #secmet #bioinformatics

www.biorxiv.org/content/10.1...

In a large community effort with 50 coauthors, we analyzed the same set of marine dissolved organic matter samples across 24 laboratories via non-targeted LC-MS/MS, to check if we get comparable data.
If you want to check it out, you can find our preprint here:
doi.org/10.26434/che...

Thanks! And yes, depending on the reagent and pH, you will have some ion suppression and the sensitive will drop. To bypass that, I would run the initial runs without infusion/pH modulation.

Thanks so much to everybody who made this interdisciplinary project possible. And epically the editor and the three reviewers at @natcomms.nature.com for their throughout positive feedback.

Implementing the MCheM setup is pretty easy, and all reagents and hardware components are commercially available and relatively cheap.
MCheM data analysis is supported in @mzmine.bsky.social @gnps2.bsky.social and SIRIUS (@brightgiant.bsky.social) and free for academic researchers.

Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling - Nature Communications To improve annotation in non-targeted metabolomics studies, authors develop a Multiplexed Chemical Metabolomics (MCheM) platform, combining post-column derivatization with integrated data processing. ...

New paper from the group. Together with Chambers Hughes, Giovanni Vitale and our amazing collaborators, we developed a multiplexed chemical metabolomics workflow to assign functional groups in non-targeted LC-MS/MS data:

www.nature.com/articles/s41...

Behind the paper story:
go.nature.com/45ljV4d

Thanks Gabriel :)

Thanks Don! Will post about the new work here and on our webpage www.functional-metabolomics.com/publication

Thanks a lot Tri :)

Thanks a lot Manuel!

Super excited that I’ve been selected as a Simons Early Career Investigator in Aquatic Microbial Ecology and Evolution. We will explore how marine microbes shape the production, transformation, and fate of dissolved organic matter.
Thanks so much @simonsfoundation.org
We can’t wait to get started!

www.grainger.com/product/SMC-...

I looked into it for a long time, happy to chat about details. I was close to buying one, but acilities finally increased the pressure to 110 psi. Was definitely worth the fight. Passive N2 generator works like a charm.

#mzmine 4.7 is now available!

This release brings our most significant improvement in memory efficiency to date, unlocking new capabilities for analyzing large-scale datasets.

Join us for a live software demo at our booth today and tomorrow at 12:00/noon during #ASMS2025

We are pretty stoked that our paper on chemical shifts in kelp forests in the Gulf of Maine made it onto the front cover of ‪@science.org
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️

🎉 Fantastic News 🎉

Our CMFI Cluster of Excellence @unituebingen.bsky.social receives funding extension for the next seven years.

Spokesperson Andreas Peschel @andreaspeschel.bsky.social: "We can now advance our research into resistance mechanisms and new antimicrobial agents!"

shorturl.at/rcK1A

AutoMLST2: a web server for phylogeny and microbial taxonomy Abstract. Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology

Happy to announce that our „newest old tool“ autoMLST2.0 is out and published. You need an accurate and easy to use tool to build #phylogenetictrees from #bacterialgenomes: academic.oup.com/nar/advance-...