ArticleBriefings in bioinformatics2023
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers, 3 of them syntheses that pooled it.
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Who cites it
93 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Metabolic phenotyping combined with transcriptomics metadata fortifies the diagnosis of early-stage Hepatocellular carcinoma.Journal of advanced research · 2025Pooled it
- Metabolomics Analysis as a Tool in Periodontitis Diagnosis: A Systematic Review.Clinical and experimental dental research · 2025Pooled it
- Metabolome panels as potential noninvasive biomarkers for primary glomerulonephritis sub-types: meta-analysis of profiling metabolomics studies.Scientific reports · 2023Pooled it
- Metabolomics in Microbial Genetic Resource Conservation: From Strain Identity to Functional Preservation.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Plasma proteomic profiling of septic shock and acute pancreatitis identifies shared signatures and disease-specific pathways.Scientific reports · 2026Article
- Metabolomics identifies tissue-specific trends in butter clams (Saxidomus gigantea) across a subarctic fjord-type estuarine system.Marine environmental research · 2026Article
- Awassi Ancestry-Associated Serum Metabolomic Signatures Reveal Immune-Metabolic Features Related to Health Robustness in Dairy Sheep.Veterinary sciences · 2026Article
- High-Quality Predicted Metabolite-Pathway Annotations Expand Pathway Coverage and Increase Enriched Pathway Detection Across Metabolomics Datasets.Metabolites · 2026Article
- Influence of sire fertility on the metabolism of in vitro produced embryos.Reproduction & fertility · 2026Article
- A Reporting Guideline for Observational Studies in Metabolomic Epidemiology: Explanation and Elaboration of the Strobe-MetEpi Checklist.Research square · 2026Article
- Revealing the Flavor and Metabolite Differences of Chinese Sweet Rice Wine Fermented with Diverse Rice Varieties Using GC-IMS and UPLC-MS/MS.Foods (Basel, Switzerland) · 2026Article
- Integrated Metabolomics of Processing Residues fromMolecules (Basel, Switzerland) · 2026Article
- Comprehensive Metabolomic Analysis of Saliva Using SWATH-DIA Reveals Systemic Metabolic Adaptations to Exercise.ACS omega · 2026Article
- Lipidomics of skin tissues from different hair types of Inner Mongolia cashmere goats.BMC veterinary research · 2026Article
- Metabolic reprogramming and functional trade-offs during domestication of Sechium edule.Scientific reports · 2026Article
- Leveraging untargeted metabolomics in combination with machine learning to uncover novel insights into bladder cancer.Cancer & metabolism · 2026Article
- Stage-specific nutritional blueprints of date fruit revealed by integrated LC-MS metabolomics and ICP-OES profiling.NPJ science of food · 2026Article
- Functional lipid analysis via index-based lipidomics profile: a new computational module in LipidOne.Bioinformatics (Oxford, England) · 2026Article
- Persistent effects of early-life arsenic exposure inEnvironmental science. Processes & impacts · 2026Article
- Seasonal Changes in the Seminal Plasma Proteome of the Crab-Eating Fox (Journal of proteome research · 2026Article
33 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
backgroundGlobal or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses to exposures or interactions with microbial communities. However, biological interpretation of global metabolomics data remains a daunting task. Recent years have seen growing applications of pathway enrichment analysis based on putative annotations of liquid chromatography coupled with mass spectrometry (LC-MS) peaks for functional interpretation of LC-MS-based global metabolomics data. However, due to intricate peak-metabolite and metabolite-pathway relationships, considerable variations are observed among results obtained using different approaches. There is an urgent need to benchmark these approaches to inform the best practices.
resultsWe have conducted a benchmark study of common peak annotation approaches and pathway enrichment methods in current metabolomics studies. Representative approaches, including three peak annotation methods and four enrichment methods, were selected and benchmarked under different scenarios. Based on the results, we have provided a set of recommendations regarding peak annotation, ranking metrics and feature selection. The overall better performance was obtained for the mummichog approach. We have observed that a ~30% annotation rate is sufficient to achieve high recall (~90% based on mummichog), and using semi-annotated data improves functional interpretation. Based on the current platforms and enrichment methods, we further propose an identifiability index to indicate the possibility of a pathway being reliably identified. Finally, we evaluated all methods using 11 COVID-19 and 8 inflammatory bowel diseases (IBD) global metabolomics datasets.
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