metaboprep v2: Broadening the application of the metaboprep beyond metabolomics

High-throughput multiplex assays for metabolomics and proteomics offer opportunities for biomarker discovery and disease stratification in epidemiological research. The complexity of these datasets requires robust, standardized and transparent preprocessing workflows to ensure reproducibility and comparability across studies. We present an updated and enhanced version of the metaboprep R package. Originally designed for metabolomics data, it has now been extended to support proteomics datasets from platforms such as Olink(R) and SomaScan(R). This release introduces a user-friendly, modular, object-oriented architecture using Rs S7 system, enabling improved input format flexibility, streamlined report generation and increased compatibility with other third-party tools. The updated pipeline is structured in three parts: data import, filtering and summary, and output generation. This structure provides a reproducible yet customizable framework for pre-analysis data preparation with utility across multiple omics platforms and particular value in supporting multi-cohort epidemiological research. Availability and implementationThe metaboprep package is implemented in R and freely available at: https://github.com/MRCIEU/metaboprep.