REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PSMA4 (1:1,000)	Enzo Life Sciences	Cat# PW8115; RRID: AB_2171569
PSMB5 (1:1,000)	Thermo Fisher Scientific	Cat# PA1-977; RRID: AB_2172052
PSMC2 (1:1,000)	Santa Cruz Biotechnology	Cat# sc-166972; RRID: AB_10611067
PSMB6 (1:1,000)	Thermo Fisher Scientific	Cat# PA1-978; RRID: AB_2172197
PSMD1 (1:1,000)	Santa Cruz Biotechnology	Cat# sc-514809
Anti-β-actin antibody (1:5,000)	Merck	Cat# A1978 RRID: AB_476692
6x-His tag monoclonal antibody (1:3,000)	Thermo Fisher Scientific	Cat# MA1-21315 RRID: AB_557403
PSMD4 (1:1,000)	Thermo Fisher Scientific	Cat# PA5-17259 RRID: AB_10978153
Goat anti-rabbit IgG (H + L) secondary antibody, HRP (1:10,000)	Thermo Fisher Scientific	Cat# 31460 RRID: AB_228341
Goat anti-mouse IgG, peroxidase conjugated, H + L (1:10,000)	Merck	Cat# AP124P RRID: AB_90456
Chemicals, peptides, and recombinant proteins
DMEM	Welgene	Cat# LM001-05
RPMI-1640	Welgene	Cat# LM011-01
l-glutamine	Welgene	Cat# LS 002-01
Gibco fetal bovine serum	Thermo Fisher Scientific	Cat# 12483020
Gibco Opti-MEM	Thermo Fisher Scientific	Cat# 31985070
Lipofectamine 3000 transfection reagent	Thermo Fisher Scientific	Cat# L3000075
Penicillin-streptomycin	Welgene	Cat# LS 202-02
Dulbecco’s phosphate-buffered saline (D-PBS)	Welgene	Cat# LB001-02
Puromycin	Cayman Chemical	Cat# 13884
suc-LLVY-AMC	Bachem	Cat# I-1395
1.5 mL microcentrifuge tube	Tarsons	Cat# T500010-N
Tris base	Merck	Cat# 77-86-1
Hydrochloric acid	Daejung Chemicals	Cat# 4090-4400
Glycerine	Daejung Chemicals	Cat# 4066-4400
Magnesium chloride anhydrous	Daejung Chemicals	Cat# 5504-4405
Adenosine 5′-triphosphate (ATP) disodium salt	Bio Basic	Cat# AB0020
Dithiothreitol (DTT)	Thermo Fisher Scientific	Cat# R8061
Tobacco etch virus (TEV) protease	Thermo Fisher Scientific	Cat# 12575015
Bovine serum albumin	Bovogen	Cat# BSAS0.05
Aprotinin	AG Scientific	Cat# A-1420
Leupeptin hemisulfate	AG Scientific	Cat# L-1165
Pepstatin A	AG Scientific	Cat# P-1519
Sodium chloride	Daejung Chemicals	Cat# 7548-4105
Potassium chloride	Daejung Chemicals	Cat# 6566-4400
EDTA	Daejung Chemicals	Cat# 4000-4405
Tween 20	Duksan General Science	Cat# 4892
ATPγS (adenosine-5'-(γ-thio)-triphosphate, tetralithium salt)	Jena Bioscience	Cat# NU-406-25
Polybrene	Merck	Cat# TR-1003-G
Sodium dodecyl sulfate (SDS)	Kanto	Cat# 37203-11
Urea	Merck	Cat# U1250-1KG
Iodoacetamide	Merck	Cat# I1149-5G
Sequencing grade modified trypsin	Promega	Cat# V5111
Sodium chloride solution	Merck	Cat# S5150-1L
Ammonium bicarbonate	Merck	Cat# 09830-500G
Formic acid (LCMS grade)	Thermo Fisher Scientific	Cat# AAB-A117-50
Acetonitrile (LCMS grade)	Thermo Fisher Scientific	Cat# A955212
Tris-HCl, pH 8.5	Nippon Gene	Cat# 316-90405
Water (HPLC grade)	Thermo Fisher Scientific	Cat# W54
Water (LCMS grade)	Thermo Fisher Scientific	Cat# W64
UltraPure SDS solution,	Thermo Fisher Scientific	Cat# 24730020
Trifluoroacetic acid	Thermo Fisher Scientific	Cat# 85183
indexed Retention Time (iRT)	Biognosys	Cat# 43891
Ammonium hydroxide	Merck	Cat# 5438300250
Protein LoBind tubes	Eppendorf	Cat# 0030108116
Empore SDB-RPS extraction disks	Thermo Fisher Scientific	Cat# 13-110-022
QSP low-retention pipette tips	Thermo Fisher Scientific	Cat# TLR070-Q
Methanol (LCMS grade)	Thermo Fisher Scientific	Cat# A456-4
Minisart NML surfactant-free cellulose acetate standard syringe filter	Sartorius	Cat# S6534-FMOSK
LCMS certified clear glass screw neck total recovery vial	Waters	Cat# 600000671CV
Critical commercial assays
NuPAGE 3%–8% Tris-acetate protein gels	Thermo Fisher Scientific	Cat# EA0375BOX
Novex Tris-glycine native running buffer (10X)	Thermo Fisher Scientific	Cat# LC2672
Novex Tris-glycine native sample buffer (2X)	Thermo Fisher Scientific	Cat# LC2673
Amicon Ultra-0.5 centrifugal filter unit	Merck	Cat# UFC5010BK
BioMag streptavidin	Bangs Laboratories	Cat# BM551
Pierce BCA protein assay kit	Thermo Fisher Scientific	Cat# 23221
Experimental models: Cell lines
Human: A549	KCLB	Cat# 10185
Human: A549-PSMB5-HB	Choi et al.	N/A
Human: A549-PSMD14-HB	Choi et al.	N/A
Human: HEK293-GP2	Takara Bio	Cat# 631458
Recombinant DNA
Plasmid: pVSV-G	Addgene	Cat# 14888
Plasmid: pQCXIP-PSMB5-HB	Choi et al.	N/A
Plasmid: pQCXIP-PSMD14-HB	Choi et al.	N/A
Software and algorithms
MaxQuant (version 1.6.1.0 and above)	Max Planck Institute of Biochemistry	https://www.maxquant.org/
Perseus (version 1.6.15.0 and above)	Max Planck Institute of Biochemistry	https://maxquant.net/perseus/
Xcalibur (version 4.5)	Thermo Fisher Scientific	N/A
BioRender	BioRender.com	N/A
Other
Dounce tissue grinder, 15 mL	Wheaton	Cat# 357544
MagJET separation rack	Thermo Fisher Scientific	Cat# MR02
Cell scraper	SPL Life Sciences	Cat# 90031
Cooling microcentrifuge	LaboGene	Cat# 1730R
Tube rotator	SeouLin Bioscience	Cat# SLRM-3
Water bath	JSR	Cat# JSWB-11T
Mini gel tank	Thermo Fisher Scientific	Cat# A25977
5 mL syringe	Koreavaccine	Cat# S15-27-167
ChemiDoc MP imaging system	Bio-Rad	Cat# 12003154
Power supply	Major Science	Cat# MP-310
PVDF membrane	Merck	Cat# IPVH00010
15 mL tube	SPL Life Sciences	Cat# 50215
96-well black plate	SPL Life Sciences	Cat# 30296
Tecan infinite m200 fluorometer	Tecan
Whatman membrane filters nylon (pore size 0.2 μm, diam. 47 mm)	Whatman	Cat# SL.MCE02047A
Size-exclusion chromatography columns (Superose 6 Increase 10/300 GL)	Cytiva	Cat# 29-0915-96
Orbitrap Exploris 480 mass spectrometer	Thermo Fisher Scientific	Cat# BRE725539
UltiMate 3000 RSLCnano system	Thermo Fisher Scientific	Cat# ULTIM3000RSLCNANO
Acclaim PepMap C18 reversed phase HPLC column	Thermo Fisher Scientific	Cat# 160454
Analytical EASY-Spray column	Thermo Fisher Scientific	Cat# ES903
Ultrasonic bath	Branson	Cat# CPX5800
Thermomixer compact	Eppendorf	N/A
CentriVap benchtop centrifugal vacuum concentrator with glass lid	Labconco	Cat# 7810015