Figure 3.

Highly complementary protein identifications observed by using EndoPro or trypsin. (A) Overview of the overlap in proteins identified by using the different proteases and varying digestion conditions as listed in Table 2, illustrating how complementarity increases when cleaving with EndoPro at different conditions. The smallest overlap, 35%, is observed between EndoPro and trypsin. (B, C) Reproducibility of (B) Trypsin and (C) EndoPro technical replicate analyses, revealing a robust overlap of around 65%. (D) When comparing all unique protein groups identified in at least three out of four technical replicates, 30% of the proteins that are reproducibly identified using EndoPro are not identified in tryptic lysates.