Supplementary Figure 1: Ape1, example of a protein degradation sentinel.

Mature Ape1 (mApe1, blue) is produced from precursor Ape1 (pApe1, grey) when the propeptide region containing a vacuolar targeting sequence (red) is cleaved by proteinase B (Pep4). Cleavage, and thus the production of mApe1, is induced upon the activation of autophagy. The ratio of tApe1/pApe1 can be used to report on autophagy. A decrease or no regulation of pApe1 abundance combined with an increase in tApe1 abundance (i.e. a tApe1/pApe1 ratio >1) indicates a shift toward mApe1 and thus activation of autophagy. NH₂ and COOH indicate the amino- and carboxy-termini of Ape1, respectively. In this study, pApe1 and mApe1 were counted as two protein species and quantified by SRM. For quantification, six peptides were retained from total Ape1 (tApe1) that are present in both forms, and pApe1 was represented by a peptide spanning the cleavage site. Detection of the peptide spanning the cleavage site could not be confirmed by the heavy-isotope labelled surrogate peptide spike-in experiment (Online Methods ) in the chosen conditions, but should be targeted in future experiments involving different sets of samples and conditions.