Data analysis was performed using Perseus49 and R software environments. Phosphopeptide intensities were transformed (log2), and significantly regulated phosphopeptides identified by ANOVA (adj. p < 0.05) and Dunnett’s post hoc test (p < 0.05 Ctr vs DOX, untreated vs inhibitors). Enrichment of gene ontology annotation (GOBP, GOMF, GOCC, KEGG, Pfam) and enrichment of kinase-substrate motifs (PhosphoSitePlus)50 was performed using a Fisher exact test with Benjamini-Hochberg used for truncation (FDR < 0.02). Motif analysis was performed of phosphopeptides regulated in both treatments using IceLogo51. KinasePA52 was used to infer kinase activity in treatments vs controls53.

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