Daniel Petras

Daniel Petras

@daniel-petras.bsky.social

Dad, Punk Rocker, Scientist, Ocean Lover. Working with the Functional Metabolomics Lab on developing mass spec tools to understand microbial communities. www.functional-metabolomics.com

271 followers224 following31 posts

Daniel Petras reposted

Mariana M. 🍉
@deerenoir.bsky.social

Could the chemicals in your furniture or food packaging be reshaping our oceans? 🌊 My latest story for @eos.org explores new research showing that industrial pollutants are now widespread across the globe, even in coral reefs once considered pristine. Take a look! 🤿 🪸 eos.org/articles/hav...

eos.orgHave We Been Focusing on the Wrong Ocean Pollutants? This Study Maps What We’ve Been Missing - EosA global analysis of more than 2,300 seawater samples found that largely unmonitored industrial compounds are widespread across oceans and may be changing crucial biological and carbon cycling process...
Daniel Petras
@daniel-petras.bsky.social

Our new paper on the presence of xenobiotics in marine dissolved organic matter just come out. Thanks to Jarmo Kalinski and our awesome collaborators, we were able to reanalyze more than 20 public LC-MS/MS datasets from seawater and ask how many anthropogenic compounds we can detect. rdcu.be/e8q6C

Daniel Petras
@daniel-petras.bsky.social

We hope this work provides new insights into how human activity can shape the global DOM pool and identifies targets for future studies to absolutely quantify and assess the cumulative effects of xenobiotics on ecosystem health and planetary processes.

Daniel Petras
@daniel-petras.bsky.social

Our new paper on the presence of xenobiotics in marine dissolved organic matter just come out. Thanks to Jarmo Kalinski and our awesome collaborators, we were able to reanalyze more than 20 public LC-MS/MS datasets from seawater and ask how many anthropogenic compounds we can detect. rdcu.be/e8q6C

Daniel Petras
@daniel-petras.bsky.social

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.

Daniel Petras
@daniel-petras.bsky.social

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.

Daniel Petras
@daniel-petras.bsky.social

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.

Daniel Petras
@daniel-petras.bsky.social

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.

Daniel Petras
@daniel-petras.bsky.social

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.

Daniel Petras reposted

Vardilab
@vardilab.bsky.social

🌊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 >>

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

Daniel Petras reposted

Johannes Rainer
@jorainer.bsky.social

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

Phili@philouail.bsky.social

🚀 New release: Metabonaut v1.4.0 is here! 1️⃣ New integration with the notame package for robust feature selection. 2️⃣ Added GNPS2 FBMN export for molecular networking. Explore the updates: rformassspectrometry.github.io/Metabonaut/ #Metabolomics #RStats #OpenScience #MassSpec #Bioconductor

rformassspectrometry.github.ioExploring and Analyzing LC-MS DataThis resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages.

Daniel Petras reposted

Ákos T Kovács
@evolvedbiofilm.bsky.social

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...

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

Daniel Petras reposted

Steffen Neumann
@sneumann.bsky.social

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.

doi.orgxcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software EcosystemHigh-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.

Daniel Petras reposted

Nadine Ziemert
@nadineziemert.bsky.social

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

pubs.acs.orgDiscovery and Heterologous Expression of the Soil Metagenome-Derived Lasso Peptide Metanodin with an Unprecedented Ring StructureCulture-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.
Daniel Petras
@daniel-petras.bsky.social

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

Pieter Dorrestein@pieterdorrestein.bsky.social

Such awesome day today at UC-Riverside. Got to spend time with two of my science children and their team (science grandchildren). Just so fun thanks to Ming for the pic. And got to go biking with @func-metabo-lab.bsky.social

Daniel Petras reposted

Nadine Ziemert
@nadineziemert.bsky.social

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...

biorxiv.orgPhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymesPhylogenetic 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...
Daniel Petras
@daniel-petras.bsky.social

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!

Simons Foundation@simonsfoundation.org

Congratulations to our six new 2025 Simons Early Career Investigators in Aquatic Microbial Ecology and Evolution! See full list: www.simonsfoundation.org/2025/07/01/a... #science @systemsecology.bsky.social @daniel-petras.bsky.social @kendraturkkubo.bsky.social

simonsfoundation.orgAnnouncing the 2025 Simons Early Career Investigators in Aquatic Microbial Ecology and EvolutionThe Simons Foundation and Simons Foundation International have named six scientists as 2025 Simons Early Career Investigators in Aquatic Microbial Ecology and Evolution. The two-year awards are intend...

Daniel Petras reposted

mzio
@mzio-gmbh.bsky.social

#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

Daniel Petras reposted

Functional Metabolomics Lab
@func-metabo-lab.bsky.social

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! ✌️✌️✌️

Science Magazine@science.org

Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests. Learn more in this week's issue of Science: scim.ag/4dwzl8j

Daniel Petras reposted

Cluster of Excellence CMFI
@cmfi.bsky.social

🎉 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

cmfi.uni-tuebingen.deCMFI Enters Second Funding Period | CMFI NewsThe members of CMFI can breathe a sigh of relief: On January 1, 2026, the Tübingen Cluster of Excellence will enter its second funding period with a duration of seven years. This was announced by the ...

Daniel Petras reposted

Nadine Ziemert
@nadineziemert.bsky.social

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-...

academic.oup.comAutoMLST2: a web server for phylogeny and microbial taxonomyAbstract. Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology

Daniel Petras reposted

Mingxun Wang
@mingxunwang.bsky.social

Thanks @ucriverside.bsky.social for featuring our work! news.ucr.edu/articles/202...

news.ucr.eduNew computer language helps spot hidden pollutantsCourtesy of UC Riverside, biologists and chemists have a new programming language to uncover previously unknown environmental pollutants and other information at breakneck speed – without requiring th...
Mingxun Wang@mingxunwang.bsky.social

I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.

Daniel Petras reposted

Mingxun Wang
@mingxunwang.bsky.social

I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.

Daniel Petras reposted

Mingxun Wang
@mingxunwang.bsky.social

I am excited to share this new paper out in JPR - "MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data." This work introduces the MS-RT method to assess MS/MS clustering accuracy on metabolomics data. doi.org/10.1021/acs....

doi.orgMS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics DataThe clustering of tandem mass spectra (MS/MS) is a crucial computational step to deduplicate repeated acquisitions in data-dependent experiments. This technique is essential in untargeted metabolomics, particularly with high-throughput mass spectrometers capable of generating hundreds of MS/MS spectra per second. Despite advancements in MS/MS clustering algorithms in proteomics, their performance in metabolomics has not been extensively evaluated due to the lack of database search tools with false discovery rate control for molecule identification. To bridge this gap, this study introduces the MS1-retention time (MS-RT) method to assess MS/MS clustering performance in metabolomics data sets. Here, we validate MS-RT by comparing MS-RT to established proteomics clustering evaluation approaches that utilize database search identifications. Additionally, we evaluate the performance of several MS/MS clustering tools on metabolomics data sets, highlighting their advantages and drawbacks. This MS-RT method and the MS/MS clustering tool benchmarking will provide valuable real world practical recommendations for tools and set the stage for future advancements in metabolomics MS/MS clustering.
Daniel Petras
@daniel-petras.bsky.social

Very important read about the discussion on in-source fragments in LC-MS/MS based metabolomics. By reanalyzing data from 30,000 authentic standards @yelabiead.bsky.social @adafede.bsky.social @pieterdorrestein.bsky.social et al. show that ISFs are substantially less that what Giera et al. reported 👌

BioMassSpec@realbiomassspec.bsky.social

Discovery of metabolites prevails amid in-source fragmentation #NatMetab www.nature.com/articles/s42...

nature.comDiscovery of metabolites prevails amid in-source fragmentation - Nature MetabolismNature Metabolism - Discovery of metabolites prevails amid in-source fragmentation

Daniel Petras reposted

Pieter Dorrestein
@pieterdorrestein.bsky.social

I can’t think of a better group to learn metabolomics data science from.

Functional Metabolomics Lab@func-metabo-lab.bsky.social

Good news: We will have another summer school on non-targeted metabolomics this year! Organized by Martin Hansen and Scott Jarmusch, this year's summer school will be hosted at DTU in Copenhagen from August 18-22, inc. a summer camp style accommodation option at DTU. Sign up: tinyurl.com/NTMS2025

Daniel Petras reposted

Michael Witting
@metabomichael.bsky.social

I'm happy to share my latest article published today. A nice collaboration with Aiko and Sven from Bruker Daltonics. #metabolomics #lipidomics #celegans doi.org/10.1007/s113...

doi.orgPhosphorylated glycosphingolipids are commonly detected in Caenorhabditis elegans lipidomes - MetabolomicsIntroduction The identification of lipids is a cornerstone of lipidomics, and due to the specific characteristics of lipids, it requires dedicated analysis workflows. Identifying novel lipids and lipi...

Daniel Petras reposted

EMN Metabolomics Society
@emn-metsoc.bsky.social

🚨 Webinar Reminder! 🚨 Don’t forget to join us for our first webinar of the year: “Learning From Repository-Scale Untargeted Metabolomics Data” 📅 Date: 22 January 🕒 Time: 3 PM UTC #MetabolomicsSociety #MetSoc #Metabolomics #ECR #TeamMassSpec #EMNMetSoc

EMN Metabolomics Society@emn-metsoc.bsky.social

🎉 First webinar for 2025! On 22 January at 3pm UTC, we will host Dr Wout Bittremieux who will deliver a talk on an approach to untargeted metabolomics data annotation! ✒️ Register here for free: tinyurl.com/2v654vp9 We look forward to seeing you there 👋

Daniel Petras reposted

Michael Marty
@michaelmarty.bsky.social

Really excited to release a beta version of UniDec 8.0! The coolest feature is a new AI-based charge assignment for isotopic resolution data. It's performing a little better than Thrash/Xtract but way faster. Try out IsoDec if you are doing top-down! github.com/michaelmarty...

github.comRelease UniDec Version 8.0.0 · michaelmarty/UniDecVersion 8.0.0 UniDec. Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications. Check out a video tutorial: https://www.youtube.com/watch?v=e33...

Daniel Petras reposted

Cluster of Excellence CMFI
@cmfi.bsky.social

Congrats to Lisa Maier, Board Member at the CMFI/University of Tuebingen, for being selected #50ScientistsThatInspire by Cell Press👏 In a Q&A she explains what drives her research and why we sometimes have to go beyond conventional approaches to find novel solutions. www.cell.com/news-do/50-i...

cell.comMicrobiologist Lisa Maier says we must go beyond conventional approaches to find novel solutionsAdvice on finding inspiration in day-to-day life and embracing one’s unique personality traits as strengths rather than weaknesses from Dr. Maier.

Daniel Petras reposted

Functional Metabolomics Lab
@func-metabo-lab.bsky.social

We had a blast at the #ecometabolomics workshop @UniCologne last week. Thanks so much for organizing this awesome event @C_Sanchez_Arcos and for the great contribution and inspiring interactions with all participants and instructors. This was a lot of fun!