Water-based deparaffinization is a ‘green’ alternative. (A) Total protein extracted after deparaffinization with either water (depW) or xylene (depX) (n = 5, unpaired t-test, p = 0.54). (B) Intra-method %CVs based on quantified proteins, median %CV are given. (C) Pearson correlation plot based on all proteins quantified by both methods. (D) Volcano plot highlighting proteins significantly enriched by either method (Benjamini–Krieger multiple hypothesis testing, FDR 1%). Cytosolic ribosomal proteins significantly enriched with depX are shown in orange. EIF4E, EGFR, and AKT1S1 are highlighted in dark grey.