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

Journal article, 2025

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.