Mitochondrial-derived peptides (MDPs) represent a recently recognized class of bioactive microproteins encoded by short open-reading frames within the mitochondrial genome. Unlike nuclear-encoded peptides, MDPs originate from mitochondrial DNA and function as retrograde signaling molecules, communicating metabolic status from mitochondria to the nucleus. Among the identified MDPs, Humanin and MOTS-c have emerged as critical regulators of metabolic homeostasis, insulin sensitivity, and stress responses. For research facilities investigating metabolic disease, aging, and mitochondrial biology, understanding their distinct mechanisms of action and analytical considerations is essential.