Urea

LB broth and LB agar were from Amresco (Solon, OH). Urea was from Teknova (Hollister, CA). LC-MS pure reagents (water, ethanol, acetonitrile, and methanol) were purchased from J.T. Baker (Radnor, PA). Gel-electrophoresis reagents were from Bio-Rad (Berkley, CA). Iodoacetamide (IAA) was purchased from MP Biomedicals (Solon. OH). All other reagents are from Sigma-Aldrich (St. Louis, MO) unless specified. The gels used for electrophoresis were from Genscript Biotech Corporation (Piscataway, NJ). Separation occurred on a Mighty Small II from Hoefer Inc. (Holliston, MA) and gels were imaged with a Bio-Rad Gel-Doc EZ Imager. DNA Miniprep spin filters were purchased from Bioneer Corporation (Oakland, CA) and the S-Trap mini devices were from Protifi (Huntington, NY). At the time of publication 200 Miniprep columns from Bioneer have a US price of $115 including DNA reagents and bulk miniprep columns from Epoch Life Science (http://www.epochlifescience.com/) can be obtained for $0.42 each without reagents. Hydrophilic–lipophilic balance (HLB) solid phase extraction (SPE) cartridges (10 mg) from Waters (Milford, MA) were used to desalt peptide samples prior to analysis on a Q-Exactive HF from Thermo Fisher Scientific (San Jose, CA) or an ultrafleXtreme MALDI-TOF from Bruker Scientific LLC (Billerica, MA).

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 described^{29 (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.