ReviewMetabolites2022
A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.
Review in Metabolites, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021-2025).Analytical chemistry · 2026Review
- A Reporting Guideline for Observational Studies in Metabolomic Epidemiology: Explanation and Elaboration of the Strobe-MetEpi Checklist.Research square · 2026Article
- Article
- An international consensus on core reproducibility items in research.PLoS biology · 2026Article
- MeTime: an R package for reproducible longitudinal metabolomics data analysis.Bioinformatics advances · 2026Article
- Reference-guided computational framework identifies microenvironment metabolic subtypes and targets using pan-cancer single-cell datasets.Genome medicine · 2025Article
- Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.Journal of the American Society for Mass Spectrometry · 2025Article
- Serum metabolic profiling analysis of chronic gastritis and gastric cancer by untargeted metabolomics.Annals of medicine and surgery (2012) · 2025Article
- Implementation of FAIR Practices in Computational Metabolomics Workflows-A Case Study.Metabolites · 2024Article
- MetaboLights: open data repository for metabolomics.Nucleic acids research · 2024Article
- The epidemiology of errors in data capture, management, and analysis: A scoping review of retracted articles and retraction notices in clinical and translational research.Journal of clinical and translational science · 2024Article
- An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.Journal of the American Society for Mass Spectrometry · 2023Article
- Untargeted Metabolomic Analysis of Lactation-Stage-Matched Human and Bovine Milk Samples at 2 Weeks Postnatal.Nutrients · 2023Article
- Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux.Nature communications · 2023Article
- Applications of Omics Technology for Livestock Selection and Improvement.Frontiers in genetics · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.