Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment14					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
LDTP08401	All trans-polyprenyl-diphosphate synthase PDSS2 (PDSS2)				C71	20.0
LDTP09200	FAD synthase (FLAD1)				C499	20.0
LDTP12405	Fructose-2,6-bisphosphatase TIGAR (TIGAR)				C161	20.0
LDTP17384	Lysine-specific demethylase RSBN1L (RSBN1L)				C280	20.0
LDTP09598	Mitochondrial coenzyme A diphosphatase NUDT8 (NUDT8)				C207	20.0
LDTP01220	Mitochondrial-processing peptidase subunit beta (PMPCB)				C265	20.0
LDTP03401	Multifunctional protein CAD (CAD)				C73	20.0
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	20.0
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	13.8
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	10.3
LDTP00758	Thioredoxin-like protein 1 (TXNL1)				C34	7.3
LDTP06320	[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial (PDK1)				C71	4.4
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	4.2
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	3.8
LDTP02074	Aldehyde dehydrogenase, mitochondrial (ALDH2)				C319	3.3
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	3.2
LDTP10973	Thioredoxin, mitochondrial (TXN2)				C90	3.2
LDTP02502	Thioredoxin (TXN)				C32	3.1
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	3.1
LDTP15290	5'-nucleotidase domain-containing protein 3 (NT5DC3)				C276	2.8
LDTP10320	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A (TRMT61A)				C209	2.7
LDTP13980	Methionine-R-sulfoxide reductase B2, mitochondrial (MSRB2)				C105	2.7
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	2.5
LDTP00481	Ubiquitin/ISG15-conjugating enzyme E2 L6 (UBE2L6)				C98	2.5
LDTP12405	Fructose-2,6-bisphosphatase TIGAR (TIGAR)				C114	2.2
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.9
LDTP04572	Dipeptidyl peptidase 1 (CTSC)				C258	1.9
LDTP03859	V-type proton ATPase catalytic subunit A (ATP6V1A)				C138	1.9
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.7
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.7
LDTP04547	Nuclear pore complex protein Nup98-Nup96 (NUP98)				C1312	1.7
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	1.7
LDTP19669	Threonine synthase-like 1 (THNSL1)				C324	1.6
LDTP18330	Haloacid dehalogenase-like hydrolase domain-containing 5 (HDHD5)				C392	1.6
LDTP03770	Alpha-adducin (ADD1)				C68	1.6
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	1.6
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C758	1.6
LDTP00479	Histone acetyltransferase type B catalytic subunit (HAT1)				C101	1.6
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	1.5
LDTP01055	6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2 (PFKFB2)				C158	1.5
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.5
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.4
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.4
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C312	1.4
LDTP09126	Probable aminopeptidase NPEPL1 (NPEPL1)				C81	1.4
LDTP01707	Thioredoxin domain-containing protein 12 (TXNDC12)				C66	1.3
LDTP10785	Ubiquitin carboxyl-terminal hydrolase 28 (USP28)				C171	1.3
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.3
LDTP15427	Ribonuclease P protein subunit p25-like protein (RPP25L)				C131	1.3
LDTP11639	RNA exonuclease 4 (REXO4)				C382	1.2
LDTP03496	Protein PML (PML)				C389	1.2
LDTP03316	DNA replication licensing factor MCM3 (MCM3)				C119	1.2
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.2
LDTP10774	Elongation factor G, mitochondrial (GFM1)				C153	1.2
LDTP07110	Putative transferase CAF17, mitochondrial (IBA57)				C170	1.2
LDTP12363	Lysophosphatidic acid phosphatase type 6 (ACP6)				C267	1.2
LDTP03258	Thymidylate kinase (DTYMK)				C117	1.2
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C190	1.1
LDTP11059	ADP-ribose glycohydrolase MACROD1 (MACROD1)				C186	1.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.1
LDTP05346	Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial (ALDH6A1)				C317	1.1
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	1.1
LDTP03163	Sterol carrier protein 2 (SCP2)				C71	1.1
LDTP12313	Putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 (ALG13)				C86	1.1
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.1
LDTP01141	E3 ubiquitin-protein ligase BRE1B (RNF40)				C890	1.1
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.1
LDTP09962	Ubiquitin carboxyl-terminal hydrolase 7 (USP7)				C223	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.0
LDTP02223	Cathepsin B (CTSB)				C211	1.0
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.0
LDTP12227	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial (MCCC2)				C216	1.0
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	1.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C57	1.0
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.0
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.0
LDTP04262	Alanine--tRNA ligase, cytoplasmic (AARS1)				C773	1.0
LDTP00642	DNA-directed RNA polymerase I subunit RPA34 (POLR1G)				C86	1.0
LDTP18123	Isochorismatase domain-containing protein 2 (ISOC2)				C114	1.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	1.0
LDTP04374	Dynamin-2 (DNM2)				C27	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP05943	Myotubularin-related protein 1 (MTMR1)				C117	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.0
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.0
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	0.9
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	0.9
LDTP03163	Sterol carrier protein 2 (SCP2)				C307	0.9
LDTP04232	4-trimethylaminobutyraldehyde dehydrogenase (ALDH9A1)				C288	0.9
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	0.9
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	0.9
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	0.9
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	0.9
LDTP03258	Thymidylate kinase (DTYMK)				C163	0.9
LDTP15311	Deaminated glutathione amidase (NIT1)				C165	0.8
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	0.8
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	0.8
LDTP05859	Integrin-linked protein kinase (ILK)				C346	0.8
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.8
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.8
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	0.8
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	0.7
LDTP04438	Succinate-semialdehyde dehydrogenase, mitochondrial (ALDH5A1)				C340	0.7
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.7
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	0.7
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	0.6
LDTP04471	Ribosomal protein S6 kinase alpha-3 (RPS6KA3)				C436	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP05252	Clathrin heavy chain 1 (CLTC)				C870	20.0
LDTP00501	Exportin-1 (XPO1)				C528	20.0
LDTP05511	Cytoskeleton-associated protein 4 (CKAP4)				C100	11.2
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	3.2
LDTP02735	G2/mitotic-specific cyclin-B1 (CCNB1)				C238	2.6
LDTP05591	Nuclear cap-binding protein subunit 1 (NCBP1)				C44	2.0
LDTP13498	Nuclear pore complex protein Nup50 (NUP50)				C151	1.8
LDTP13824	Voltage-dependent anion-selective channel protein 3 (VDAC3)				C65	1.7
LDTP04801	Gasdermin-D (GSDMD)				C268	1.6
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.4
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.2
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.0
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.9
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	0.8
LDTP10642	Chloride intracellular channel protein 6 (CLIC6)				C487	0.8
LDTP01689	Chloride intracellular channel protein 3 (CLIC3)				C22	0.8
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	20.0
LDTP03280	COUP transcription factor 2 (NR2F2)				C326	4.9
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.7
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.4
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.4
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.3
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.0

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C629	20.0
LDTP05257	Receptor expression-enhancing protein 5 (REEP5)				C18	20.0
LDTP12412	Reticulon-4 (RTN4)				C1101	20.0
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	20.0
LDTP07205	Telomere-associated protein RIF1 (RIF1)				C2298	20.0
LDTP13515	Zinc finger protein 346 (ZNF346)				C68	20.0
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C439	5.9
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	5.8
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	5.7
LDTP01532	ZW10 interactor (ZWINT)				C54	5.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	5.0
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	4.6
LDTP00306	Pescadillo homolog (PES1)				C272	3.8
LDTP05867	Treacle protein (TCOF1)				C38	3.6
LDTP13622	NFU1 iron-sulfur cluster scaffold homolog, mitochondrial (NFU1)				C213	3.5
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C819	3.4
LDTP17182	Uncharacterized protein C3orf38 (C3orf38)				C308	3.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	3.1
LDTP05867	Treacle protein (TCOF1)				C1298	3.0
LDTP13402	Dynactin subunit 4 (DCTN4)				C258	3.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	2.9
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	2.7
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C532	2.5
LDTP08094	Wings apart-like protein homolog (WAPL)				C160	2.4
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	2.3
LDTP12753	Succinate dehydrogenase assembly factor 2, mitochondrial (SDHAF2)				C83	2.2
LDTP09626	Heterogeneous nuclear ribonucleoprotein L-like (HNRNPLL)				C464	2.2
LDTP12443	Anillin (ANLN)				C712	2.1
LDTP14250	Cytoplasmic dynein 1 light intermediate chain 1 (DYNC1LI1)				C51	2.1
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	1.9
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.8
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.8
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.7
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.7
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.6
LDTP13088	Protein IMPACT (IMPACT)				C195	1.6
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.6
LDTP04487	Cyclin-H (CCNH)				C244	1.6
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.5
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.5
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.5
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.5
LDTP13580	Coronin-1C (CORO1C)				C420	1.4
LDTP06276	MAD2L1-binding protein (MAD2L1BP)				C124	1.4
LDTP08018	Zinc finger CCCH-type antiviral protein 1 (ZC3HAV1)				C645	1.4
LDTP03615	Heterogeneous nuclear ribonucleoprotein H (HNRNPH1)				C267	1.3
LDTP11235	Protein PAXX (PAXX)				C180	1.3
LDTP13906	Polymerase delta-interacting protein 2 (POLDIP2)				C143	1.3
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.3
LDTP04952	Heterogeneous nuclear ribonucleoprotein K (HNRNPK)				C132	1.3
LDTP12800	Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PPP4R2)				C22	1.3
LDTP04092	Crk-like protein (CRKL)				C249	1.3
LDTP15896	Ashwin (C2orf49)				C10	1.2
LDTP14215	Small ribosomal subunit protein mS40 (MRPS18B)				C128	1.2
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	1.2
LDTP06330	Plectin (PLEC)				C4574	1.2
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	1.1
LDTP04434	Host cell factor 1 (HCFC1)				C1872	1.1
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.1
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	1.0
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	1.0
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.0
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.0
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.0
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.0
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C90	1.0
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	0.9
LDTP10864	Calponin-2 (CNN2)				C164	0.9
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	0.8
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	0.8
LDTP00229	Copper transport protein ATOX1 (ATOX1)				C12	0.7
LDTP18494	Tropomodulin-3 (TMOD3)				C132	0.5

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.