Data analysis strategies for targeted and untargeted LC-MS metabolomic studies: Overview and workflow

Sensitivity is a challenge in untargeted methods, and many metabolites are detected in some but not other samples, which limits the utility of many analytes for modelling.

“Sensitivity is another challenge in untargeted methods, and many metabolites are detected in some but not other samples122–124, which limits the utility of many analytes for modelling.”

Targeted methods have better sensitivity but are limited by predefining a set of metabolites to look for, greatly reducing the number of features detected and precluding the discovery of new metabolites.

“Targeted methods have better sensitivity but are limited by predefining a set of metabolites to look for in the experiment, greatly reducing the number of features detected and precluding the discovery of new metabolites122–124.”

Untargeted metabolomics methods have the advantage of detecting many thousands of metabolite features; however, most compounds detected via mass spectrometry and NMR are orphan compounds whose structure has not been identified.

“Untargeted metabolomics methods have the advantage of being able to detect many thousands of metabolite features; however, most compounds detected via mass spectrometry and NMR are orphan compounds, that is, their structure has not been identified122–124.”

In both targeted and untargeted methods, even for confidently identified compounds, the biological processes that generated them are often poorly understood.

“In both targeted and untargeted methods, even for confidently identified compounds, the biological processes that generated them are often poorly understood122–125.”