Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment38					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
LDTP00414	Dual specificity mitogen-activated protein kinase kinase 7 (MAP2K7)				C131	20.0
LDTP02055	Thymidylate synthase (TYMS)				C199	20.0
LDTP03258	Thymidylate kinase (DTYMK)				C163	5.7
LDTP03258	Thymidylate kinase (DTYMK)				C117	4.4
LDTP10973	Thioredoxin, mitochondrial (TXN2)				C90	3.6
LDTP11059	ADP-ribose glycohydrolase MACROD1 (MACROD1)				C186	3.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	3.4
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	2.8
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	2.8
LDTP05346	Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial (ALDH6A1)				C317	2.4
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	2.4
LDTP03496	Protein PML (PML)				C389	2.2
LDTP03859	V-type proton ATPase catalytic subunit A (ATP6V1A)				C138	2.1
LDTP02502	Thioredoxin (TXN)				C32	2.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C54	2.0
LDTP09126	Probable aminopeptidase NPEPL1 (NPEPL1)				C81	2.0
LDTP02223	Cathepsin B (CTSB)				C211	1.8
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.8
LDTP15370	Pseudouridylate synthase RPUSD2 (RPUSD2)				C246	1.7
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.7
LDTP00481	Ubiquitin/ISG15-conjugating enzyme E2 L6 (UBE2L6)				C98	1.6
LDTP13980	Methionine-R-sulfoxide reductase B2, mitochondrial (MSRB2)				C105	1.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.6
LDTP14159	Ubiquitin carboxyl-terminal hydrolase 16 (USP16)				C205	1.5
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.5
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.4
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.4
LDTP03770	Alpha-adducin (ADD1)				C68	1.4
LDTP08436	Interferon regulatory factor 2-binding protein 1 (IRF2BP1)				C363	1.3
LDTP04547	Nuclear pore complex protein Nup98-Nup96 (NUP98)				C1312	1.3
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.3
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.3
LDTP12313	Putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 (ALG13)				C86	1.3
LDTP06320	[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial (PDK1)				C71	1.3
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.2
LDTP18123	Isochorismatase domain-containing protein 2 (ISOC2)				C114	1.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.2
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.2
LDTP05480	Amidophosphoribosyltransferase (PPAT)				C100	1.2
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C312	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.1
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.1
LDTP00479	Histone acetyltransferase type B catalytic subunit (HAT1)				C101	1.1
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.1
LDTP07407	Desumoylating isopeptidase 1 (DESI1)				C108	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C190	1.0
LDTP01707	Thioredoxin domain-containing protein 12 (TXNDC12)				C66	1.0
LDTP06211	Caspase-8 (CASP8)				C360	1.0
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.0
LDTP10320	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A (TRMT61A)				C209	1.0
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.0
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.0
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.0
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.0
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	0.9
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	0.9
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	0.9
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.9
LDTP04374	Dynamin-2 (DNM2)				C27	0.9
LDTP03316	DNA replication licensing factor MCM3 (MCM3)				C119	0.9
LDTP08808	E3 SUMO-protein ligase PIAS4 (PIAS4)				C326	0.9
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.9
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C57	0.9
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.8
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	0.8
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	0.8
LDTP10785	Ubiquitin carboxyl-terminal hydrolase 28 (USP28)				C171	0.8
LDTP18330	Haloacid dehalogenase-like hydrolase domain-containing 5 (HDHD5)				C392	0.8
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	0.8
LDTP09962	Ubiquitin carboxyl-terminal hydrolase 7 (USP7)				C223	0.8
LDTP04262	Alanine--tRNA ligase, cytoplasmic (AARS1)				C773	0.7
LDTP04232	4-trimethylaminobutyraldehyde dehydrogenase (ALDH9A1)				C288	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP05252	Clathrin heavy chain 1 (CLTC)				C870	20.0
LDTP13824	Voltage-dependent anion-selective channel protein 3 (VDAC3)				C65	20.0
LDTP00501	Exportin-1 (XPO1)				C528	2.1
LDTP02735	G2/mitotic-specific cyclin-B1 (CCNB1)				C238	1.8
LDTP04801	Gasdermin-D (GSDMD)				C268	1.8
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.7
LDTP05591	Nuclear cap-binding protein subunit 1 (NCBP1)				C44	1.2
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.1
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.1
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.0
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.8
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.3
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.0
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	20.0
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	20.0
LDTP12412	Reticulon-4 (RTN4)				C1101	20.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C819	4.6
LDTP13622	NFU1 iron-sulfur cluster scaffold homolog, mitochondrial (NFU1)				C213	3.5
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	3.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	3.0
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	2.6
LDTP18494	Tropomodulin-3 (TMOD3)				C132	2.6
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	2.5
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	2.5
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	2.4
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	2.3
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	2.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C518	2.2
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	2.1
LDTP05867	Treacle protein (TCOF1)				C1298	2.0
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	2.0
LDTP12571	LanC-like protein 2 (LANCL2)				C187	2.0
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.8
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	1.8
LDTP14179	Cytosolic Fe-S cluster assembly factor NUBP2 (NUBP2)				C72	1.7
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.7
LDTP04092	Crk-like protein (CRKL)				C249	1.6
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.5
LDTP05772	FAS-associated death domain protein (FADD)				C98	1.5
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.5
LDTP12443	Anillin (ANLN)				C712	1.5
LDTP10864	Calponin-2 (CNN2)				C164	1.5
LDTP09626	Heterogeneous nuclear ribonucleoprotein L-like (HNRNPLL)				C464	1.5
LDTP11235	Protein PAXX (PAXX)				C180	1.4
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	1.4
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	1.4
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	1.4
LDTP13580	Coronin-1C (CORO1C)				C420	1.4
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.4
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	1.4
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.3
LDTP10252	Elongator complex protein 4 (ELP4)				C218	1.3
LDTP04434	Host cell factor 1 (HCFC1)				C1872	1.3
LDTP03615	Heterogeneous nuclear ribonucleoprotein H (HNRNPH1)				C267	1.2
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.2
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.2
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.1
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C439	1.1
LDTP05867	Treacle protein (TCOF1)				C38	1.1
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	1.1
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.1
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.0
LDTP07624	Biogenesis of lysosome-related organelles complex 1 subunit 3 (BLOC1S3)				C168	1.0
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.0
LDTP04952	Heterogeneous nuclear ribonucleoprotein K (HNRNPK)				C132	1.0
LDTP12800	Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PPP4R2)				C22	1.0
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.0
LDTP14215	Small ribosomal subunit protein mS40 (MRPS18B)				C128	1.0
LDTP04487	Cyclin-H (CCNH)				C244	1.0
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.0
LDTP15896	Ashwin (C2orf49)				C10	0.9
LDTP08018	Zinc finger CCCH-type antiviral protein 1 (ZC3HAV1)				C645	0.9
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.7
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	0.3

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.