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Related Experiment Video

Updated: Jun 13, 2026

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Published on: March 14, 2013

xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem.

Philippine Louail^1,2, Carl Brunius³, Mar Garcia-Aloy⁴

¹Institute for Biomedicine, Eurac Research, 39100 Bolzano, Italy.

Analytical Chemistry

|December 8, 2025

Summary

This summary is machine-generated.

The xcms R package offers enhanced scalability and interoperability for untargeted metabolomics data preprocessing. These advancements support reproducible, large-scale experiments and integrate with broader R/Bioconductor tools.

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Area of Science:

Metabolomics
Bioinformatics
Computational Biology

Background:

High-quality data preprocessing is critical for untargeted metabolomics.
Increasing data scale and complexity necessitate robust software solutions.
The xcms R package has been a widely used tool for LC-MS data preprocessing since 2005.

Purpose of the Study:

To present recent advancements in the xcms R package.
To position xcms as a central component of a modular metabolomics software ecosystem.
To highlight improvements in scalability and interoperability.

Main Methods:

Utilizing the R programming language and Bioconductor framework.
Implementing open-source, community-driven development.
Enhancing scalability for large-scale experiments.

Main Results:

xcms now offers enhanced scalability for processing thousands of samples.
Improved interoperability with downstream analysis platforms and R/Bioconductor packages.
Expanded resources including tutorials and documentation for user support.

Conclusions:

xcms advancements solidify its role in modern metabolomics research.
The package empowers users to build customizable and reproducible workflows.
Integration with the broader R ecosystem extends the utility of xcms.