TraceMetrix: a traceable metabolomics interactive analysis platform

Abstract

Metabolomics data analysis is a multifaceted process often constrained by limited data sharing and a lack of transparency, which hinders reproducibility of results. While existing bioinformatics tools address some of these challenges, achieving greater simplicity and operational clarity remains essential for fully leveraging the potential of metabolomics. Here, we introduce TraceMetrix, a web-based platform designed for interactive traceability in metabolomics data analysis. TraceMetrix provides a flexible management system for both raw and derived data, enabling comprehensive tracking of file origins and destinations throughout the whole analysis pipeline. The platform documents the software and parameters used across four key modules, from raw data preprocessing, data cleaning, statistical analysis to functional analysis, enabling users to easily track critical factors influencing result accuracy. By mapping upstream and downstream relationships for nearly 19 analytical functions, TraceMetrix ensures end-to-end traceability, viewable interactively online or exportable as detailed reports. To address the limitations of single-machine environments in processing large-scale datasets, TraceMetrix is deployed on a high-performance computing cluster for efficient batch processing. Using a non-targeted metabolomics dataset, we demonstrated its traceability function to optimize parameter selection, successfully reproducing the analysis process and validating the original study's findings. TraceMetrix integrates traceability across data, software, and processes, significantly enhancing reproducibility in metabolomics research. The platform supports diverse applications and is freely available at https://www.biosino.org/tracemetrix.