Fig. 1.

Determination of optimal digestion conditions for ProAlanase, using HeLa cell lysate. Specificity plots reflecting the average C-terminal amino acid frequency in ProAlanase-digested HeLa cell lysates (n = 2) at the different pH (B) and time (A) of digestion. Unspecific MaxQuant search settings were used for specificity estimation. C-terminal amino acid frequency on the y axis was calculated as a relative count of identified peptides, containing the specific C-terminal residue. Average proportion of unique peptides identified in ProAlanase digests of HeLa cell lysates (n = 2) carrying 0, 1, 2, 3 or 4 missed cleavage sites, using enzyme-specific settings for peptide-to-sequence matching. The comparison is done for the different pH (D) and time (C) of digestion. Digestion conditions, considered as optimal, are marked with the *. Unique peptides sequences identi_ed in ProAlanase digests of HeLa cell lysates (n = 4) at the optimal digestion conditions (E).