KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PTMScan Ubiquitin Remnant Motif (K-ε-GG) Kit	Cell Signaling Technology	Cat#5562
Protein A Plus Ultralink resin	ThermoFisher Scientific	Cat#53142
Chemicals, Peptides, and Recombinant Proteins
Bortezomib	ApexBio Technology	Cat#A2614
Antimycin A	Sigma-Aldrich	Cat#A8674
Oligomycin A	Sigma-Aldrich	Cat#75351
Tandem Mass Tags	ThermoFisher Scientific	Cat#90406
cOmplete, Mini Protease Inhibitor Cocktail	Sigma-Aldrich	Cat#11836153001
PhosSTOP, Phosphatase Inhibitor	Sigma-Aldrich	Cat#4906837001
EPPS	Sigma-Aldrich	Cat#E9502
Rapigest SF Surfactant	Glixx Laboratories	Cat#GLXC-07089
2-Chloroacetamide	Sigma-Aldrich	Cat#C0267
Aprotinin	Roche	Cat#10981532001
Leupeptin	Roche	Cat#11034626001
AEBSF Protease Inhibitor	Gold Biotechnology	Cat#A-540
TCEP	Sigma-Aldrich	Cat#646547
NEM	Sigma-Aldrich	Cat#E3876
PR-619	Selleck Chem	Cat# S7130
Critical Commercial Assays
BCA Protein Assay Kit	ThermoFisher Scientific	Cat#23225
Quantitative Colorimetric Peptide Assay	Thermo Fisher Scientific	Cat#23275
High pH Reversed-Phase Peptide Fractionation Kit	ThermoFisher Scientific	Cat#84868
Deposited Data
Raw Mass Spectrometry Data Files	This paper; Proteome Xchange	PXD004628
Experimental Models: Cell Lines
HCT-116, Human colorectal carcinoma	ATCC	Cat#CCL-247
HeLa Flp-In T-REx (HFT) PARKINWT	Ordureau et al., 2014	N/A
HeLa Flp-In T-REx (HFT) PARKIN S65A	Ordureau et al., 2014	N/A
HeLa Flp-In T-REx (HFT) PINK1−/−	Ordureau et al., 2014	N/A
Experimental Models: Organisms/Strains
Mouse: C57BL/6	Jackson Laboratories	Stock#000664
Software and Algorithms
In-house mass spectrometry data analysis software	Huttlin et al., 2010	N/A
SEQUEST	Eng et al., 1994	N/A
Perseus	Tyanova et al., 2016	http://www.coxdocs.org/doku.php?id=perseus:start
R	https://www.r-project.org/	N/A
Other
Orbitrap Fusion Mass Spectrometer	ThermoFisher Scientific	Cat#IQLAAEGAAPFADBMBCX
Orbitrap Fusion Lumos Mass Spectrometer	ThermoFisher Scientific	Cat#IQLAAEGAAPFADBMBHQ
Easy-nLC 1000	ThermoFisher Scientific	Cat#LC120