Steffen Neumann

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.

This celebrates 20 years since #MassBank started in Japan. The new system developed at @ipbhalle.bsky.social went live in June at both massbank.eu and massbank.jp. We had >20 releases of reference spectra submitted by not only the #metabolomics, #exposomics and #EnvironmentalScience communities.

Project 14 here at the #BioHackEU25 will work to assess and improve the state of #mzTab-M for #Metabolomics over the next few days. Plus having fun meeting all the other attendees here near Berlin

🚀 We’ve launched the new MassBank! Now live at massbank.eu & massbank.jp — redesigned with a faster backend, better search, and powerful tools for exploring & sharing mass spectral data. Enjoy the fresh experience! Feedback and ideas welcome, please post them on github.com/MassBank/Mas...

Thanks @jorainer.bsky.social , that is the culmination of twenty wonderful years at @ipbhalle.bsky.social !

Zhixu Ni presenting LipidCXSMILES developed together with @egonw.mastodon.social.ap.brid.gy and #epilipidnet and #lipidmaps here at #MetSoc2025 bridging real lipid chemical structures, and the uncertainty because MS gives only so much structural hints.

As mentioned in my talk yesterday at #MetSoc2025,@schymane@mstdn.social and myself offered a bottle of wine to the winners of #CASMI 2016 contest.
Pleased to confirm eventual delivery of a fine Czech Merlot to www.linkedin.com/in/tobias-ki... for winningCategory 3: Full Information.

Hi, in case your phone didn't pick up the QR code to the slides of my Hitch-Hikers Guide to Computational Metabolomics talk this morning at #Metabolomics2025, featuring #xcms, #massbank, not #metfrag but #CASMI and #MetFamily, please find them at doi.org/10.5281/zeno...

Lange Nacht, die Wissen schafft am 4. Juli am IPB. Feines Experimentierprogramm für Groß und Klein. Mit Quiz und Preisen und Nachwuchsforscherdiplom. Mehr Infos: www.ipb-halle.de/oeffentlichk...

matchms is a wonderful fit in the microservice architecture of the MassBank software rewrite. We even have a REST interface to query MassBank programmatically.

Data has a life-cycle, and justifies that it is maintained (like software), rather than just dumped when the paper comes out.
P.S.: I think mastodon allows longer messages ;-)

2) Instead of downloading data from somewhere, massaging/fixing stuff, and doing your own analysis, get the word back upstream what didn't work with the original data ! Have the tool / data people fix things upstream, so that the next person has less pain than you did, converging on interoperability

Prepare your data for submission right away! No need to publish same time, but if your analysis is based on the same information that'll be published later, you ensure that it works for one person (you!), and certainly that'll be interoperable for others as well.

Hi, two ideas: 1) if it is about your own experimental data, be your first re-user ! Instead of doing the experiment, organising and massaging (format wise!) your data so you can analyse it, and eventually publish the data in a repository like MetaboLights, Metabolomics Workbench, ...

#Vacancy: We're offering a position as a Research associate in #ComputationalMetabolomics in @sneumann 's group!

More information: ipb-halle.de/en/career/jo...

#Bioinformatics #Metabolomics #ComputationalBiochemistry #scijobs Please share this post !