Metabolite Annotation through Stable Isotope Labeling

Stable isotope labeling (SIL) is a powerful tool for probing cellular metabolism and has been increasingly employed for metabolite annotation in mass spectrometry-based metabolomics. Herein, we outline the principles and methods of designing and performing SIL-based experiments in metabolomics studies. Further, we summarize different SIL approaches and highlight recent examples of their use for metabolite annotation, including biological feature recognition, degenerate feature annotation, elemental composition determination and metabolite structure elucidation, across diverse biological systems. Throughout, the opportunities, open challenges, and potential pitfalls of each SIL workflow are discussed. Finally, we summarize and compare the recently developed software tools for the analysis of SIL-based metabolomics data.