Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web

Stable isotope tracing is a crucial technique for understanding
the metabolic wiring of biological systems, determining metabolic
flux through pathways of interest, and detecting novel metabolites
and pathways. Despite the potential insights provided by this technique,
its application remains limited to a small number of targeted molecules
and pathways. Because previous software tools usually require chemical
formulas to find relevant features, and the data are highly complex,
especially in untargeted metabolomics and when the downstream reactions
and metabolites are poorly characterized. We report here Khipu version
2 and its new user-friendly web application. New functions are added
to enhance analyzing stable isotope tracing data including metrics
that evaluate peak enrichment in labeled samples, scoring methods
to facilitate robust detection of intensity patterns and integrated
natural abundance correction. We demonstrate that this approach can
be applied to untargeted metabolomics to systematically extract isotope-labeled
compounds and annotate the unidentified metabolites.