We are currently analyzing the induction of autophagy upon heart tissue samples, and I would like to know if there is a way to distinguish the non-selective autophagy than the selective one (particularly mitophagy).
you can analyze selective mitophagy by interaction/co-localization study of mitochondrial marker protein and the autophagy specific adaptor protein LC3II.
If you need a detailed explanation, look at thoae references. An experiment that could demonstrate selective autophagy (if positive results, if negative you will still not know) is if degradation or autophagosome recruitment is abolished by KO or KD of mitophagy receptors e.g. NIX, BNIP3, OPTN, NDP53,