A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research

Abstract

Clinical metabolomics emerged as a novel approach for biomarker discovery with the translational potential to guide next-generation therapeutics and precision health interventions. However, reproducibility in clinical research employing metabolomics data is challenging. Checklists are a helpful tool for promoting reproducible research. Existing checklists that promote reproducible metabolomics research primarily focused on metadata and may not be sufficient to ensure reproducible metabolomics data processing. This paper provides a checklist including actions that need to be taken by researchers to make computational steps reproducible for clinical metabolomics studies. We developed an eight-item checklist that includes criteria related to reusable data sharing and reproducible computational workflow development. We also provided recommended tools and resources to complete each item, as well as a GitHub project template to guide the process. The checklist is concise and easy to follow. Studies that follow this checklist and use recommended resources may facilitate other researchers to reproduce metabolomics results easily and efficiently.

Keywords: checklist; clinical research; metabolomics; reproducibility; reproducible workflow; reusable data.

Figure 1

Overview of metabolomics study workflow. Workflow includes steps of sample preparation, data acquisition, data processing, and data interpretation. Each step has multiple substeps, and each substep has several techniques that can be used. Minimum information checklists were proposed to guide metadata reporting for purpose of reproducibility improvement. Some example items included in existing minimum checklists are shown in blue column of figure.

Figure 2

Checklist for computational reproducibility improvement of clinical metabolomics research. Eight items are included, which are categorized to reusable data sharing items and reproducible computational workflow items. All items are about actions that a researcher needs to take for reproducibility improvement. Detailed explanation and example resources are also included on right side of figure.