xcms at 20 and still in peak form: Anchoring a complete metabolomics data preprocessing and analysis software ecosystem

09 June 2025, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing dataset 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 has maintained 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 the 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.

Keywords

open software development
LC-MS preprocessing
computational mass spectrometry

Supplementary materials

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Description
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Supplementary Table S1.
Description
Table listing packages present in the xcms toolkit and their respective information (description, status of development, repository link), therefore expanding Figure 2.
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Supplementary Figure S2.
Description
Figure presents a way to integrate xcms with other tools to achieve an end-to-end workflow. Adapted from the Metabonaut website.
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