#xcms
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
June 26, 2025 at 9:10 AM
Great work from @philouail.bsky.social 🙌

#xcms now fully integrated into @bioconductor.bsky.social 💪

👉 #metabolomics #MassSpectrometry #rstats
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.
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.
doi.org
December 9, 2025 at 7:11 AM
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.
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.
doi.org
December 8, 2025 at 8:26 PM
🚀 New in Metabonaut: tested xcms on a 4,000+ sample LC-MS dataset — all on a laptop! 💻
Fully reproducible + now possible thanks to dev improvements in xcms.
Vignette: rformassspectrometry.github.io/Metabonaut/a...

Big thanks to @jorainer.bsky.social

#RStats #MassSpec #OpenScience #Metabonaut
Large Scale Data Preprocessing with xcms
rformassspectrometry.github.io
June 4, 2025 at 11:14 AM
@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🙏)
June 26, 2025 at 9:32 AM
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...
June 25, 2025 at 9:15 AM
Updates in 🦕 #xcms #rstats #metabolomics package:

👉 retention time alignment against external data set
👉 chromatographic peak quality metrics
👉 performance improvements

Available in @bioconductor.bsky.social release 3.21 🚀

Up next: memory-saving analysis of very large data sets 😎

#TeamMassSpec
April 18, 2025 at 6:59 AM
Courses du jour:

🛣️ 🇧🇪 Delirium Grand Prix de Wallonie
💩 🇬🇧 Hope Supercross #3
🪨 🇮🇱 Epic Israel XCMS
September 17, 2025 at 6:00 AM
The central message behind our two recent papers in @NatMetabolism @MolSystBiol

•• If you can’t identify it with XCMS-METLIN,
highly likely it is ISF (in-source fragmentation) ••

Both papers are open access
www.nature.com/articles/s42...
www.embopress.org/doi/full/10....
December 4, 2024 at 3:57 PM
Unexpected growth on the #METLIN front, now reaching 960K molecular standards with MS/MS natural product additions. 960K METLIN currently available online via XCMS-METLIN. xcmsonline.scripps.edu
@Molsystbio doi.org/10.1038/s443...
April 4, 2025 at 1:22 PM
The simplicity of precursor ion filtering combined with MS/MS matching to deconvolve data on XCMS-METLIN's 935K+ molecular standards @MolSystBiol doi.org/10.1038/s443...
XCMS-METLIN local now available at massconsortium.com
November 26, 2024 at 10:44 PM
xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem #AC pubs.acs.org/doi/10.1021/...
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. Mode...
pubs.acs.org
December 8, 2025 at 8:08 PM
Twenty years in the making, the #XCMS-METLIN integrated platform is now available with the complete #METLIN MS/MS 935K+ molecular standards database.
Available as a local version on your own personal computer.
For information visit massconsortium.com
November 22, 2024 at 7:16 PM
Thanks Gary! Also, we have to thank you for keeping #xcms open-source and for adding it to @bioconductor.bsky.social back in 2006 🙌
December 12, 2025 at 4:25 PM
And in the same 📚, a chapter on untargeted #metabolomics data analysis with #xcms by Mar Garcia-Aloy, me and Pietro Franceschi ☺️ link.springer.com/protocol/10....
January 15, 2025 at 6:12 PM
A free version just posted—courtesy of #Nature.
Lipidomics (via #XCMS / #METLIN) reveals α-tocopherol (vitamin E) as a key player in ferroptosis resistance in cancer.

t.co/HMJSLuTAnM

#Lipidomics #CancerResearch #Ferroptosis #VitaminE
June 17, 2025 at 9:36 PM
🚀 Starting the week by sharing Metabonaut:

rformassspectrometry.github.io/Metabonaut/

A collection of comprehensive tutorials for LC-MS/MS data analysis in R! Learn raw data processing, annotation & stats with xcms, RforMassSpectrometry & Bioconductor—all reproducible & community-driven! #rstats
Exploring and Analyzing LC-MS Data
This resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages.
rformassspectrometry.github.io
March 31, 2025 at 6:51 AM
www.youtube.com/watch?v=xCms...
Racist felon and pseudo-Christian Trump did another executive order. This one is about how so-called American christians are being persecuted for their faith. Spoiler alert: they aren't.
Trump's Anti-Christian Bias Executive Order Broke My Brain
YouTube video by Michael Burns
www.youtube.com
February 9, 2025 at 10:35 PM
Courses du jour:

🪨 🇪🇸 Andalucia Bike Race by Garmin XCMS
🦿 🇧🇷 Pan American Track Para Cycling Championship 2026
February 25, 2026 at 7:00 AM
I'm not familiar with it so genuinely naive question: What can it do that eg. MS-DIAL, XCMS, MZMine, OpenMS can't?
December 11, 2024 at 12:37 AM
Can only second that! Was great to give the #xcms workshop today in this beautiful lecture hall!
February 21, 2024 at 9:46 PM
Por cierto, mañana empieza esto. ¿No estáis nerviosos? 😤
September 16, 2025 at 9:55 AM
Courses du jour:

🛣️ 🇧🇪 Omloop Nieuwsblad
🪨 🇪🇸 Andalucia Bike Race by Garmin XCMS
🦿 🇧🇷 Pan American Road Para Cycling Championship 2026
February 28, 2026 at 7:00 AM