REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Dulbecco’s modified Eagle’s medium (DMEM)	Thermo Fisher Scientific	Cat#: 11995073
Dulbecco’s phosphate-buffered saline (DPBS)	Thermo Fisher Scientific	Cat#: 14190250
Gibco Trypsin-EDTA (0.25%), phenol red	Fisher Scientific	Cat#: 25-200-114
Fetal bovine serum	Avantor Seradigm	Cat#: 1500-500
Fetal bovine serum (FBS), dialyzed, US origin	Thermo Fisher Scientific	Cat#: 26400044
Penicillin-Streptomycin (10,000 U/mL)	Thermo Fisher Scientific	Cat#: 15140122
Recombinant M-CSF generated from CMG14-12 culture supernatant	Lam et al., 200019	N/A
Opti-MEM reduced serum medium	Thermo Fisher Scientific	Cat#: 31985070
LipoFexin	Lambda Biotech	Cat#: TS310
Lenti-X concentrator	Takara Bio	Cat#: 631232
Lipopolysaccharide (LPS)	InvivoGen	Cat#: tlrl-smlps
Recombinant murine IFN-γ	PeproTech	Cat#: 315-05
Cycloheximide	Fisher Scientific	Cat#: AC357420010
D-biotin	Combi-Blocks	Cat#: SS-7910
RIPA buffer with Triton|r X-100 (5×)	Fisher Scientific	Cat#: AAJ62885AE
Light isopropyl iodoacetamide alkyne (L-IPIAA)	Desai et al.6	N/A
Heavy isopropyl iodoacetamide alkyne (H-IPIAA)	Desai et al.6	N/A
Iodoacetamide alkyne (IAA)	This paper (See “before you begin”)	N/A
10× PBS	Bioland	Cat#: PBS01-02
Streptavidin agarose	Fisher Scientific	Cat#: PI20353
DL-dithiothreitol 98.0+% (DTT)	Fisher Scientific	Cat#: D107125G
Trypsin, TPCK treated	Worthington Biochem	Cat#: LS003740
CuSO4	Fisher Scientific	Cat#: BP346-500
TBTA	Click Chemistry Tools	Cat#: 1061-1G
Tert-butanol	Fisher Chemical	Cat#: A401-1
Biotin-azide	Cao et al.18	N/A
Sodium ascorbate	Spectrum Chemical	S1349
Sera-Mag SpeedBead carboxylate-modified (E3) magnetic particles	Cytiva	Cat#: 65152105050250
Sera-Mag SpeedBead carboxylate-modified (E7) magnetic particles	Cytiva	Cat#: 45152105050250
Acetonitrile	Fisher Scientific	Cat#: A998-4
MOPS	Fisher Scientific	Cat#: AAA1291422
Sodium phosphate	Fisher Scientific	Cat#: S397-500
NaCl	Fisher Scientific	Cat#: S271-500
NeutrAvidin agarose	Fisher Scientific	Cat#: PI29200
Formic acid, 99.0+%, Optima LC/MS grade	Fisher Scientific	Cat#: A117-50
UltraPure distilled water	Invitrogen	Cat#: 10977015
Dimethyl sulfoxide (DMSO)	Fisher BioReagents	Cat#: BP231-100
Urea	Fisher Chemical	Cat#: U15-3
Hex-5-yn-1-amine	Combi-Blocks	Cat#: QH-9488
Chloroacetyl chloride	Sigma-Aldrich	Cat#: 22880-100ML
Triethylamine	Fisher Scientific	Cat#: T0424500ML
Sodium iodide	Fisher Scientific	Cat#: S324-100
Acetone	Fisher Chemical	Cat#: A18-20
Anhydrous DCM	Fisher Scientific	Cat#: MDX08364
Propargylamine	Combi-Blocks	Cat#: OS-7456
Sodium triacetoxyborohydride	Fisher Scientific	Cat#: AC291821000
Acetone (13C3, 99%)	Cambridge Isotope Laboratories	Cat#: CLM-1334-1
Sodium cyanoborodeuteride	Sigma-Aldrich	Cat#: 190020
Methanol, Optima LC/MS grade	Fisher Chemical	Cat#: A456-4
Biotin-NHS	Combi-Blocks	Cat#: QA-1959
3-Azido-1-propanamine	Fisher Scientific	Cat#: 50-1742-832
Anhydrous DMF	VWR	Cat#: 200004-428
Critical commercial assays
BCA Protein Assay	Thermo Fisher Scientific	Cat#: PI23227
Experimental models: Cell lines
HEK293T	ATCC	Cat#: CRL-3216 RRID: CVCL_0045
Cre-J2 viral supernatant immortalized bone-marrow-derived macrophages	Laboratory of Stephen Smale	N/A
Recombinant DNA
FUGW-Mito-TurboID	Yan et al.1	Plasmid#: 200963
pCMV-VSV-G lentiviral packaging plasmid	Addgene	Plasmid#: 8454
pCMV-dR8.2 dvpr lentiviral packaging plasmid	Addgene	Plasmid#: 8455
Software and algorithms
FragPipe	Kong et al.,20 da Veiga Leprevost et al.,21 Yu et al.22	https://fragpipe.nesvilab.org/
Perseus	Tyanova et al.23	https://maxquant.net/perseus/
R-4.2.3	The Comprehensive R Archive Network (CRAN)	https://cran.rstudio.com/
Thermo XCalibur	Thermo Fisher Scientific	RRID: SCR_014593
230119_mouse_process.py	Yan et al.1	https://github.com/BackusLab/cysloc
Volcano_AJ-CysLOx.Rmd	This paper	https://github.com/BackusLab/cyslox_volcano
Other
CO2 cell incubator	Thermo Fisher Scientific	Cat#: 370
SpeedVac concentrator	Savant Instruments, Inc.	Serial No.: SC100-OK47429-1A
Orbitrap Eclipse Tribrid mass spectrometer	Thermo Fisher Scientific	Cat#: FSN04-10000
EASY-nLC 1200 System	Thermo Fisher Scientific	Cat#: LC140
Prelubricated 1.7 mL microcentrifuge tube	Costar	Cat#: 3207
General long-term storage cryogenic tubes	Fisher	Cat#: 03-337-7D
LN2 freezer	Thermo Scientific	Cat#: 8209
Magnetic rack	Amazon	Cat#: B0812XLPVK
Fluorescence-activated cell sorter (FACS)	BD Biosciences	BD Aria
Bulk C18 reverse-phase resin	https://dr-maisch.com/	Particle size, 1.9 m; pore size, 100 Å
100 μm inner diameter (ID) fused silica capillary	Molex	NA
Thermo Scientific SureSTART 0.3 mL glass snap top microvials for <2 mL samples, level 3 high-performance applications	Fisher Scientific	Cat#: 03-452-365
Thermo Scientific SureSTART 11 mm snap caps, level 3 high-performance applications	Fisher Scientific	Cat#: 03-452-372