Figure 2

Partial APP₆₉₅ isoform sequence and antibody efficiency. (A) Red dashed line indicates BACE1 cleavage sites (β-site is the predominant cleavage location, with the β’ site being a significantly lesser contributor). Green dashed lines show the α-secretase cleavage sites (α’ is a significantly lesser contributor). Fuchsia arrows show γ-secretase cleavage sites, that, if preceded by BACE1 cleavage at the β cleavage site, would result in Aβ₃₈, Aβ₄₀, or Aβ₄₂, respectively. Mrk61 antibody bound to Sepharose beads recognizes the neo-epitope of sAPPβ (-KM highlighted in red), whereas W0-2 antibody bound to Sepharose beads recognizes a short sequence C-terminal to the β-secretase cleavage location, which is only located in sAPPα or Aβ (green highlight), but not in sAPPβ. The APP mid-domain tryptic peptide quantified by MS is shown in blue highlight. It is a peptide common to both sAPPβ and sAPPα. Leucines that may incorporate label are shown in red. Panel created with BioRender.com. (B) Efficiency of Mrk61 immunoprecipitation showing sAPPβ in the starting material and in the supernatant of the sample after IP. Original full blot is presented in Supplementary Fig. S5A. (C) Efficiency of W0-2 immunoprecipitation showing sAPPα in the starting material and in the supernatant of the sample after IP. Original full blot is presented in Supplementary Fig. S5B. (D) Percentages of sAPPβ and sAPPα (from starting material) remaining in supernatants of the serial immunoprecipitation as measured by Meso Scale Discovery assays.