Human recombinant proteases (with catalogue numbers indicated)
were obtained from R&D Systems (Minneapolis, MN), consisting of
human recombinant cathepsin L (#952-CY-010), human recombinant cathepsin
V (#1080-CY-010), human recombinant PC1/3 (#2810-SE-010), and human
recombinant PC2 (#6018-SE-010). Protease MSP-MS assays utilized the
library of 228 14-mer peptides designed to contain all possible protease
cleavage sites, as previously described29 (link),30 (link) (peptides
synthesized by Anaspec, Fremont, CA). Assays utilized octyl-β-glucopyranoside
(Sigma-Aldrich, Darmstadt, Germany), dithiothreitol (DTT, Promega,
Madison, WI), BEH C18 packing material (Waters Corporation, Milford,
MA), acetonitrile (ACN, Fisher Chemical, Pittsburgh, PA), trifluoroacetic
acid (TFA, Fisher Chemical, Pittsburgh, PA), urea (Teknova, Hollister,
CA), and C18 for solid-phase extraction (SPE) stage-tips (3M, Maplewood,
MN). Fluorogenic proteolytic assays used the substrates Z-K-R-AMC,
Z-R-K-AMC, Z-K-K-AMC, Z-R-R-AMC, Z-L-K-R-AMC, Z-W-K-R-AMC, Z-F-K-R-AMC,
Z-Y-K-R-AMC, Z-V-K-R-AMC, Z-G-K-R-AMC, and Z-A-K-R-AMC from Genscript
(Piscataway, NH); Z-F-R-AMC was from Bachem (Vista, CA) and pERTKR-AMC
was from R&D Systems.