There are a lot of different metabolites with VIP>1 and P<0.05 in non-target results. How do I select meaningful ones?
In untargeted metabolomics results, when there are many differential metabolites that meet the screening criteria of VIP > 1 and P < 0.05, the following steps can be taken to select biologically significant metabolites:
(1) Metabolic pathway enrichment analysis: Perform pathway enrichment analysis on differential metabolites, prioritizing those in significantly enriched pathways. These metabolites usually play a central role in certain biological processes.
(2) Literature support and biological background: Review the literature to identify metabolites that have been reported to be associated with specific biological processes or diseases, confirming their biological importance and relevance.
(3) Key nodes in the metabolic network: Use metabolic network analysis tools (such as Cytoscape) to construct a metabolite interaction network and identify metabolites with high connectivity or centrality (such as high betweenness), as these are often key regulatory nodes.
(4) Significance of Fold Change: Among metabolites that meet VIP and P-value criteria, further select those with larger Fold Change (e.g., Fold Change > 1.5 or 2), as metabolites with greater changes are more likely to have biological significance.
(5) Integration of multi-omics data: If transcriptomics or proteomics data is available, select metabolites that are significant in multiple omics to ensure their relevance to the research target at multiple levels.
(6) Feasibility of experimental validation: Prioritize metabolites for which detection methods are well established and suitable for subsequent targeted quantitative validation, allowing better verification of their function or mechanism in follow-up experiments.
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