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. 2021 Nov 12;7(46):eabj0722. doi: 10.1126/sciadv.abj0722

Fig. 3. Global ubiquitylation analysis of mitochondria in neurons of PINK1 wild-type and KO neurons.

Fig. 3.

(A) Total protein abundance of membrane-enriched lysates in PINK1+/+ or PINK1−/− neurons. Fold increase for individual protein is shown in the volcano plot. The x axis specifies the fold changes, and the y axis specifies the negative logarithm to the base 10 of the t test P values [Welch’s t test (S0 = 0.585), corrected for multiple comparison by permutation-based FDR (5%)]. Proteins associated with mitochondria (MitoCarta 3.0) or MOM are indicated. (B) Abundance for phospho-Ser65 (top) or phospho-Ser57 (bottom) of ubiquitin (Ub) was quantified and plotted as fold change to untreated wild-type samples. Error bars represent SEMs (n = 3). Error bars represent SEMs (n = 3, 3, 3, and 2). (C and D) The same as (A) but diGLY-containing peptides derived from (C) PINK1+/+ or (D) PINK1−/− cells. (C) One hundred eighty-seven and 11 sites or (D) 26 and 0 sites, respectively, represent statistically significant ubiquitylated targets up-regulated or down-regulated after mitochondrial depolarization. [Welch’s t test (S0 = 1), corrected for multiple comparison by permutation-based FDR (1%)]. diGLY peptides associated with mitochondria (MitoCarta 3.0) or MOM are indicated. Square-shaped dots indicate diGLY peptides not normalized to its protein abundance (not determined).