Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment27					Competitor Info
Competitor Concentration	200 uM
In Vivo Experiment Model	Model Type			Living cell
	Derived Tissue			Breast
	Disease Model		Breast adenocarcinoma [ICD-11:2C60]
	Model Name		Human breast adenocarcinoma cells (MDA-MB-231)

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C71	20.0
LDTP10973	Thioredoxin, mitochondrial (TXN2)				C90	6.3
LDTP03859	V-type proton ATPase catalytic subunit A (ATP6V1A)				C138	4.6
LDTP02502	Thioredoxin (TXN)				C32	2.5
LDTP11059	ADP-ribose glycohydrolase MACROD1 (MACROD1)				C186	2.4
LDTP09598	Mitochondrial coenzyme A diphosphatase NUDT8 (NUDT8)				C207	2.2
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	2.2
LDTP05346	Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial (ALDH6A1)				C317	2.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.9
LDTP07407	Desumoylating isopeptidase 1 (DESI1)				C108	1.9
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.8
LDTP15290	5'-nucleotidase domain-containing protein 3 (NT5DC3)				C276	1.7
LDTP10774	Elongation factor G, mitochondrial (GFM1)				C153	1.6
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.6
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.6
LDTP01220	Mitochondrial-processing peptidase subunit beta (PMPCB)				C265	1.6
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.5
LDTP06320	[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial (PDK1)				C71	1.5
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.5
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.5
LDTP13980	Methionine-R-sulfoxide reductase B2, mitochondrial (MSRB2)				C105	1.5
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.4
LDTP12539	DNA dC->dU-editing enzyme APOBEC-3C (APOBEC3C)				C130	1.3
LDTP18330	Haloacid dehalogenase-like hydrolase domain-containing 5 (HDHD5)				C392	1.3
LDTP12363	Lysophosphatidic acid phosphatase type 6 (ACP6)				C267	1.3
LDTP08401	All trans-polyprenyl-diphosphate synthase PDSS2 (PDSS2)				C71	1.3
LDTP04547	Nuclear pore complex protein Nup98-Nup96 (NUP98)				C1312	1.3
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.3
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.2
LDTP01141	E3 ubiquitin-protein ligase BRE1B (RNF40)				C890	1.2
LDTP14159	Ubiquitin carboxyl-terminal hydrolase 16 (USP16)				C205	1.2
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.2
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.2
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.2
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.1
LDTP09962	Ubiquitin carboxyl-terminal hydrolase 7 (USP7)				C223	1.1
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.1
LDTP10785	Ubiquitin carboxyl-terminal hydrolase 28 (USP28)				C171	1.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C312	1.1
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C57	1.1
LDTP12227	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial (MCCC2)				C216	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C190	1.0
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C758	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP03316	DNA replication licensing factor MCM3 (MCM3)				C119	1.0
LDTP18123	Isochorismatase domain-containing protein 2 (ISOC2)				C114	1.0
LDTP17384	Lysine-specific demethylase RSBN1L (RSBN1L)				C280	1.0
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	0.9
LDTP04438	Succinate-semialdehyde dehydrogenase, mitochondrial (ALDH5A1)				C340	0.9
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	0.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.9
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	0.9
LDTP03770	Alpha-adducin (ADD1)				C68	0.9
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	0.8
LDTP00013	Ubiquitin-like modifier-activating enzyme 6 (UBA6)				C347	0.8
LDTP05480	Amidophosphoribosyltransferase (PPAT)				C100	0.8
LDTP03496	Protein PML (PML)				C213	0.8
LDTP02223	Cathepsin B (CTSB)				C211	0.8
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	0.7
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	0.7
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.7
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	0.7
LDTP04262	Alanine--tRNA ligase, cytoplasmic (AARS1)				C773	0.6
LDTP12405	Fructose-2,6-bisphosphatase TIGAR (TIGAR)				C161	0.6
LDTP05859	Integrin-linked protein kinase (ILK)				C346	0.6
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	0.6
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	0.6
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	0.5
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	0.5
LDTP03401	Multifunctional protein CAD (CAD)				C73	0.5
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	0.5
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	0.5
LDTP04374	Dynamin-2 (DNM2)				C27	0.5
LDTP03496	Protein PML (PML)				C389	0.5
LDTP02055	Thymidylate synthase (TYMS)				C199	0.5
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	0.5
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.5
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	0.5
LDTP12405	Fructose-2,6-bisphosphatase TIGAR (TIGAR)				C114	0.4
LDTP12313	Putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 (ALG13)				C86	0.4
LDTP06211	Caspase-8 (CASP8)				C360	0.4
LDTP05289	AMP deaminase 2 (AMPD2)				C107	0.4
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.4
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C54	0.3
LDTP03258	Thymidylate kinase (DTYMK)				C163	0.2

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	20.0
LDTP13824	Voltage-dependent anion-selective channel protein 3 (VDAC3)				C65	1.6
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	1.3
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.0
LDTP05591	Nuclear cap-binding protein subunit 1 (NCBP1)				C44	0.8
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	0.7
LDTP04801	Gasdermin-D (GSDMD)				C268	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	2.1
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.4
LDTP03280	COUP transcription factor 2 (NR2F2)				C326	1.2
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.2
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.0
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	20.0
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	2.4
LDTP13515	Zinc finger protein 346 (ZNF346)				C68	1.9
LDTP12753	Succinate dehydrogenase assembly factor 2, mitochondrial (SDHAF2)				C83	1.5
LDTP12412	Reticulon-4 (RTN4)				C1101	1.4
LDTP13622	NFU1 iron-sulfur cluster scaffold homolog, mitochondrial (NFU1)				C213	1.3
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.3
LDTP06330	Plectin (PLEC)				C4574	1.3
LDTP05867	Treacle protein (TCOF1)				C38	1.3
LDTP16117	Mediator of RNA polymerase II transcription subunit 9 (MED9)				C139	1.3
LDTP14217	Lipid droplet-regulating VLDL assembly factor AUP1 (AUP1)				C391	1.2
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.1
LDTP04487	Cyclin-H (CCNH)				C244	1.1
LDTP03615	Heterogeneous nuclear ribonucleoprotein H (HNRNPH1)				C267	1.1
LDTP15896	Ashwin (C2orf49)				C10	1.1
LDTP05257	Receptor expression-enhancing protein 5 (REEP5)				C18	1.1
LDTP14215	Small ribosomal subunit protein mS40 (MRPS18B)				C128	1.0
LDTP12443	Anillin (ANLN)				C712	1.0
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.0
LDTP05867	Treacle protein (TCOF1)				C1298	1.0
LDTP06276	MAD2L1-binding protein (MAD2L1BP)				C124	1.0
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	0.9
LDTP04952	Heterogeneous nuclear ribonucleoprotein K (HNRNPK)				C132	0.9
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	0.9
LDTP13402	Dynactin subunit 4 (DCTN4)				C258	0.8
LDTP08018	Zinc finger CCCH-type antiviral protein 1 (ZC3HAV1)				C645	0.8
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	0.8
LDTP13580	Coronin-1C (CORO1C)				C420	0.8
LDTP09650	LIM domain only protein 7 (LMO7)				C228	0.8
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	0.8
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	0.7
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	0.7
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	0.7
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	0.7
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	0.7
LDTP17182	Uncharacterized protein C3orf38 (C3orf38)				C308	0.7
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	0.7
LDTP05772	FAS-associated death domain protein (FADD)				C98	0.6
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	0.6
LDTP06046	Ribosome biogenesis protein BOP1 (BOP1)				C404	0.6
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	0.6
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	0.6
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C90	0.6
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	0.6
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	0.6
LDTP10252	Elongator complex protein 4 (ELP4)				C218	0.6
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C439	0.6
LDTP14250	Cytoplasmic dynein 1 light intermediate chain 1 (DYNC1LI1)				C51	0.6
LDTP18494	Tropomodulin-3 (TMOD3)				C132	0.6
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	0.6
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C819	0.5
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	0.5
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	0.5
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	0.5
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	0.5
LDTP01532	ZW10 interactor (ZWINT)				C54	0.5
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	0.5
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	0.4
LDTP12571	LanC-like protein 2 (LANCL2)				C187	0.4
LDTP00229	Copper transport protein ATOX1 (ATOX1)				C12	0.4
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	0.4

1	Proteome-wide covalent ligand discovery in native biological systems. Nature. 2016 Jun 23;534(7608):570-4. doi: 10.1038/nature18002. Epub 2016 Jun 15.