REAGENT or RESOURCE	SOURCE	IDENTIFIER
Cell lines
Immortalized cancer cell line (HeLa or HCT116)	ATCC CCL-2 or ATCC CCL-247
Chemicals, peptides, and recombinant proteins
Dulbecco’s modified Eagle’s medium (DMEM)	Fisher Scientific	Cat#31966047
Penicillin/streptomycin	Life Technologies	Cat#15140-122
Fetal bovine serum	Life Technologies	Cat#10270106
Lysyl endopeptidase	Fujifilm Wako	Cat#129-02541
Sequencing grade modified trypsin	Promega	Cat#V511X
MagReSyn Hydroxyl (20 mg/mL in 20% EtOH)	ReSyn Biosciences	Cat#MR-HYX010
MagReSyn Ti-IMAC HP (20 mg/mL in 20% EtOH)	ReSyn Biosciences	Cat#MR-THP010
MagReSyn Zr-IMAC HP (20 mg/mL in 20% EtOH)	ReSyn Biosciences	Cat#MR-ZHP010
Triethylammonium bicarbonate (TEAB)	Sigma-Aldrich	Cat#90360
HEPES pH 8.0	Sigma-Aldrich	Cat#H3375
Tris (2-carboxyethyl) phosphine hydrochloride (TCEP)	Sigma-Aldrich	Cat#C4706
Ammonium bicarbonate (AmmBic)	Sigma-Aldrich	Cat#T7408
Trifluoroacetic acid (TFA)	Sigma-Aldrich	Cat#302031
Formic acid (FA) – for LC-MS	Sigma-Aldrich	Cat#00940
Sodium dodecyl sulfate (SDS)	Fisher Scientific	Cat#10607443
2-Chloroacetamide (CAA)	Sigma-Aldrich	Cat#C0267
Glycolic acid (GA)	Sigma-Aldrich	Cat# 420581
Acetonitrile (MeCN) – for LC-MS	Sigma-Aldrich	Cat#1.00029
Tris-HCl	Sigma-Aldrich	Cat#PHG0002
Ammonia water (NH4OH 25% aqueous solution)	Sigma-Aldrich	Cat#1054321011
Ethanol (EtOH) > 99.9%	Sigma-Aldrich	Cat#51976
1-isopropanol or 2-propanol analysis	Sigma-Aldrich	Cat# 1070222511
TMTpro 16-plex Label Reagent	Thermo Fisher Scientific	Cat#A44520
Hydroxylamine hydrochloride (50.0%)	Thermo Fisher Scientific	Cat#90115
Critical commercial assays
Pierce Microplate BCA Protein Assay Kit - Reducing Agent Compatible	Thermo Fisher Scientific	Cat#23252
EZ PCR Mycoplasma Detection Kit	Biological Industries	Cat#20-700-20
Software and algorithms
Spectronaut		https://biognosys.com/software/spectronaut/
MaxQuant		https://www.maxquant.org/
Perseus		https://maxquant.net/perseus/
Peptide Collapse plugin		https://github.com/AlexHgO/Perseus_Plugin_Peptide_Collapse
UniProt database human	UniProt	https://www.uniprot.org/proteomes/UP000005640 Proteome ID: UP000005640
Other
Ultra-low attachment 96-well plates	Corning Costar	Cat#CLS3474
Cell scraper	TPP	Cat#99003
Micro centrifuge (1.5–2 mL tubes)	Various suppliers	N/A
Magnetic separator	Thermo Fisher Scientific	Cat#12321D
Incubator for cells	Various suppliers	N/A
Biological safety cabinet for cell culture	Various suppliers	N/A
Chemical safety cabinet	Various suppliers	N/A
Eppendorf ThermoMixer F1.5 or equivalent	Eppendorf	Cat#5384000012
SpeedVac concentrator	Thermo Fisher Scientific	Cat#SPD111V-115
Tip Horn for Model 120 Sonic Dismembrator (8-tip probe sonicator) or equivalent dry sonicator	Fisherbrand	Cat#FB4599
NanoDrop 2000 spectrophotometer	Thermo Fisher Scientific	Cat#ND-2000
Computer station with minimum requirements of used Spectronaut version	Various suppliers	N/A
KingFisher Flex (Apex, Duo Prime) system	Thermo Fisher Scientific	Cat#A31508 (5400920, 5400110)
KingFisher Flex Microtiter deep-well 96 plate	Thermo Fisher Scientific	Cat#95040460
Sep-Pak tC18 96-well plate, 40 mg sorbent per well	Waters	Cat#186003966
Extraction plate manifold for 96-well plates	Waters	Cat#186001831
Multifuge X3	Thermo Fisher Scientific	Cat#75004500
Carriers for microplates	Thermo Fisher Scientific	Cat#75003617
MultiScreenHTS HV filter plate, 0.45 μm	Merck	Cat#MSHVN4550
KingFisher Flex 96 Heating Block (compatible with deep-well microtiter plate)	Thermo Fisher Scientific	Cat#24075430
KingFisher Flex Microtiter standard 200 μL 96 plate	Thermo Fisher Scientific	Cat#97002540
KingFisher Flex 96 Heating Block (compatible with 200 μL microtiter plate)	Thermo Fisher Scientific	Cat#24075420
C18 stage tips: P200 LoBind pipette tips	Merck; 3M	Cat#CLS4154-4X960EA
C18 stage tips: Empore C18 extraction disk	Fisher Scientific	Cat#13110018
UltiMate 3000 high-performance liquid chromatography system	Thermo Fisher Scientific	N/A
Acquity CSH C18 1.7 μm × 1 mm × 150 mm column	Waters	Cat#186006935
Evosep One HPLC system	Evosep	N/A
Evosep endurance column (15 cm × 150 μm, 1.9 μm)	Evosep	EV1106
Evosep performance column (8 cm × 150 μm, 1.5 μm)
Evosep performance column (15 cm × 75 μm, 1.9 μm)	Evosep
Evosep	EV1109
EV1112
Aurora Elite column (15 cm × 75 μm, 1.7 μm)	IonOpticks	Cat#AUR3-15075C18-TS
Sonation Column Oven PRSO-V2
Butterfly heater	Sonation lab solutions
MSWil	PRSO-V2
Cat#PST-ES-BPH-20
Evosep stainless steel emitter 30 μm i.d.	Evosep	EV1086
Evosep fused silica emitter 10 μm i.d.	Evosep	EV1111
Thermo Scientific Exploris 480 mass spectrometer or any other mass spectrometer with high precision MS1 spectrum recording	Thermo Fisher Scientific