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Formalin‐fixed, paraffin‐embedded PCT‐SWATH protocol and performance. (A) Prostate FFPE tissue in a punch. (B) Acid, base, and heat treatment to reverse cross‐links. (C) Schematic protocol of FFPE PCT‐SWATH. (D) Peptide yield per milligram FFPE tissue with different Tris/HCl (pH 10.0) boiling time. (E) Number of peptides identified by the peptides prepared with different Tris/HCl boiling time. (F) Yield of peptides from 48 prostate tissue samples.
