REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit monoclonal anti-β-tubulin (dilution 1:1,000 for western blotting)	Cell Signaling Technology	Cat. #2128, RRID:AB_823664
Rabbit monoclonal anti-KAT2A (dilution 1:1,000 for western blotting)	Cell Signaling Technology	Cat. #3305, RRID:AB_2128281
Rabbit monoclonal anti-KAT2B (dilution 1:1,000 for western blotting)	Cell Signaling Technology	Cat. #3378 RRID:AB_2128409
Rabbit monoclonal anti-SIRT5 (dilution 1:1,000 for western blotting)	Cell Signaling Technology	Cat. #8782, RRID:AB_2716763
Chemicals, peptides, and recombinant proteins
Acetonitrile (Burdick & Jackson; LC-MS grade)	Honeywell	Cat. #LC015
BlpI	New England Biolabs	Cat. #R0585
BstXI	New England Biolabs	Cat. #R0113
DL-dithiothreitol (DTT)	Sigma-Aldrich	Cat. #D9779
Formic acid (FA; Fluka; Puriss.-grade)	Honeywell	Cat. #27001
Halt protease/phosphatase single-use inhibitor cocktail (100x)	Thermo Fisher Scientific	Cat. #78442
Iodoacetamide (IAA)	Sigma-Aldrich	Cat. #I1149
Nicotinamide	Sigma-Aldrich	Cat. #72340
Quick Ligation kit	New England Biolabs	Cat. #M2200
Phosphate-buffered saline (PBS; Gibson), pH 7.4 (1x)	Thermo Fisher Scientific	Cat. #10010-023
Puromycin	Santa Cruz Biotechnology	Cat. #sc-108071
Sodium chloride	VWR	Cat. #BDH9286
Trichostatin A	Cayman Chemical	Cat. #89730
Triethylammonium bicarbonate (TEAB), pH8 (1 M)	Sigma-Aldrich	Cat. #7408
Trifluoroacetic acid (TFA; HPLC-grade)	Sigma-Aldrich	Cat. #302031
Trypsin (sequencing-grade modified)	Promega	Cat. #V5111
Urea	Thermo Fisher Scientific	Cat. #29700
Water (Burdick & Jackson; LC-MS grade)	Honeywell	Cat. #LC365
Critical commercial assays
Lipofectamine 3000	Invitrogen	Cat. #L3000
Quick-DNA microprep kit	Zymo Research	Cat. #3020
ZymoPURE plasmid miniprep kit	Zymo Research	Cat. #4210
iRT kit	Biognosys	https://biognosys.com/product/irt-kit/
Pierce BCA protein assay	Thermo Fisher Scientific	Cat. #23225
PTMScan malonyl-lysine [Mal-K] kit	Cell Signaling Technology	Cat. #93872
Deposited data
Raw data and complete CRISPRi K562 cell malonylome and proteome MS datasets	N/A	MassIVE ID number: MSV000093564; ProteomeXchange ID: PXD047514 ftp://massive.ucsd.edu/v06/MSV000093564/
Experimental models: Cell lines
Human: HEK293T	ATCC	CRL-3216
Human: K562-dCas9-KRAB	Gilbert et al.3	N/A
Recombinant DNA
pCMV-dR8.91 packaging vector	Creative Biogene	Cat. #OVT2971
pMD2.G envelope vector	Addgene	RRID:Addgene_12259
pU6-sgRNA-EF1Alpha-puro-T2A-BFP	Addgene	RRID:Addgene_60955
Software and algorithms
CRISPRi-v2.1 algorithm	Horlbeck et al.4	N/A
FlowJo	Becton Dickinson & Company	https://www.flowjo.com
GraphPad Prism 6	GraphPad	https://graphpad.com/
Skyline-daily	MacLean et al.10	Skyline version 21.1.1.223; https://skyline.ms
SnapGene	Dotmatics	https://www.snapgene.com/
Spectronaut	Biognosys	Spectronaut version 15.1.210713.50606; https://biognosys.com/software/spectronaut/
Other
Acclaim PepMap 100 C18 trap column (75 μm × 2 cm, 3 μm particle size	Thermo Fisher Scientific	PN 164535
Acclaim PepMap 100 C18 analytical column (75 μm × 50 cm, 3 μm particle size	Thermo Fisher Scientific	PN 164570
Benchtop centrifuge	N/A	N/A
Empore 2215 C18 47-mm	CDS Analytical	Cat. #98-0604-0217-3EA
Flat-ended 200-μL pipette tips	N/A	N/A
Microtubes 0.65 mL	N/A	N/A
Microtubes 1.5 mL	N/A	N/A
Microtubes 2 mL	N/A	N/A
Oasis HLB 1 cc cartridges, 30 mg sorbent	Waters	Cat. #WAT058882
Orbitrap Eclipse Tribrid mass spectrometer	Thermo Fisher Scientific	N/A
Probe sonicator	N/A	N/A
Rotating mixer	N/A	N/A
SpeedVac vacuum concentrator	N/A	N/A
Thermomixer	N/A	N/A
UltiMate 3000 HPLC system	Thermo Fisher Scientific	N/A
Vacuum manifold	N/A	N/A