Jan Stanstrup

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.

@jorainer.bsky.social and @philouail.bsky.social gave a great overview of the ecosystem around #RforMassSpectrometry and #XCMS!

#MetSoc25
I am super glad they now also provide options to combine with #Python and #matchms (thanks🙏)

Our protocol paper describing our 🤱🏼MOTILITY Mother-Child Cohort: a Danish prospective longitudinal cohort study of the #infant gut #microbiome, nutrition and bowel habits has been published ✨

bmjopen.bmj.com/content/15/6/e…

Thanks to Independent Research Fund Denmark for supporting our work 🙏

Steffen @sneumann.bsky.social on the history and background of @bioconductor.bsky.social during his keynote talk at the #MetSoc2025 conference 😎

Philippine @philouail.bsky.social presenting #xcms , summary of 20 years development and recent extensions at the #MetSoc2025 conference!

#ProudPI 😎 #rstats @bioconductor.bsky.social #metabolomics #MassSpectrometry

so how's your day going?

Times are changing but order matters: Transferable prediction of small molecule liquid chromatography retention times

Authors: Fleming Kretschmer, Eva-Maria Harrieder, Michael Witting, Sebastian Böcker
DOI: 10.26434/chemrxiv-2024-wd5j8

PhD course: Introduction to Nutritional Metabolomics

The course goes through all stages of an LC-MS based untargeted metabolomics study including sample handling, pre-processing, statistics and identification.

June 30th – July 4th, 2025 in Copenhagen
phdcourses.ku.dk/DetailKursus...

#Metabolomics

And he would have gotten away with it if it wasn't for this meddling, autistic, anti-social, super-power-wielding woman!

Metabolomics Platform Manager

📣 Do you know an expert in analytical chemistry and #metabolomics 🌟 that would be excited about supporting cutting-edge research within the fields of #nutrition, #microbiome and health? (help us - retweet and like) 🙏
📍 Copenhagen
✉ Deadline: 12 January 2025 🌞
employment.ku.dk/staff/?show=...

Postdoc in Metabolomics, Microbiome, and Cardiometabolic health

📣 A 3-year #postdoc position in #Metabolomics, Microbiome, and Cardiometabolic health is now available in our group in #Copenhagen 🌟 Do you know a bright, kind and motivated candidate? (help us share, like) 🙏 ❤️

✉ Deadline: 5 January 2025 🌞
employment.ku.dk/faculty/?sho...