Metabolomics Analysis

Comprehensive analysis of metabolomics data from metabolite identification through quantification, statistical analysis, pathway interpretation, and integration with other omics layers.

Domain Reasoning

Metabolomics quantification depends critically on normalization. Total ion current (TIC) normalization corrects for sample-loading variation and works well for global abundance changes; internal standard normalization is more accurate for targeted analysis where specific metabolite concentrations matter. Missing values in a peak table may reflect signal below the detection limit — not true absence — and should be imputed or handled explicitly rather than treated as zero. Failing to account for batch effects across instrument runs is a frequent source of spurious differential metabolites.

LOOK UP DON'T GUESS

• Metabolite identities: use Metabolite_search and Metabolite_get_info to confirm names, CIDs, and HMDB IDs; never assume identity from m/z alone.
• Pathway memberships: query KEGG, MetaCyc, or Reactome tools; do not list pathways from memory.
• Disease associations: retrieve from CTD via Metabolite_get_diseases; do not infer clinical relevance without database evidence.
• CV thresholds and QC criteria: apply the values defined in this workflow (CV < 30%, blank ratio > 3x); do not override with guesses.

When to Use This Skill