Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment28					Competitor Info
Competitor Concentration	500 uM
In Vivo Experiment Model	Model Type			Cell lysate
	Derived Tissue			Breast
	Disease Model		Breast adenocarcinoma [ICD-11:2C60]
	Model Name		Human breast adenocarcinoma cell lysate (MDA-MB-231)

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP00701	D-3-phosphoglycerate dehydrogenase (PHGDH)				C369	3.0
LDTP13147	Cathepsin Z (CTSZ)				C92	3.0
LDTP02502	Thioredoxin (TXN)				C32	2.8
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	2.2
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.8
LDTP05992	Bleomycin hydrolase (BLMH)				C73	1.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.7
LDTP09598	Mitochondrial coenzyme A diphosphatase NUDT8 (NUDT8)				C207	1.7
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	1.6
LDTP11111	Tudor-interacting repair regulator protein (NUDT16L1)				C88	1.4
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	1.4
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.4
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.4
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.3
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.3
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.3
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	1.3
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.3
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	1.3
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.3
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.3
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.3
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.2
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.2
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.2
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.2
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.2
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.2
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.2
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	1.2
LDTP04424	Galactokinase (GALK1)				C182	1.2
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	1.2
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.2
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.1
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.1
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.1
LDTP06211	Caspase-8 (CASP8)				C360	1.1
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.1
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.1
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.1
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.1
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	1.1
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.1
LDTP01495	E3 ubiquitin-protein ligase UBR5 (UBR5)				C2267	1.1
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.1
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	1.1
LDTP13147	Cathepsin Z (CTSZ)				C173	1.1
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.1
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.1
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.0
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.0
LDTP03496	Protein PML (PML)				C389	1.0
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.0
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.0
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.0
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	1.0
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.0
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.0
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.0
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.0
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.0
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.0
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.0
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	1.0
LDTP05289	AMP deaminase 2 (AMPD2)				C107	1.0
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.0
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.0
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.0
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.0
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.0
LDTP04689	Adenosine kinase (ADK)				C353	0.9
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	0.9
LDTP02223	Cathepsin B (CTSB)				C319	0.9
LDTP13080	GMP reductase 2 (GMPR2)				C186	0.9
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	0.9
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.9
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	0.9
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	0.9
LDTP02223	Cathepsin B (CTSB)				C211	0.9
LDTP04374	Dynamin-2 (DNM2)				C27	0.9
LDTP02672	Elongation factor 2 (EEF2)				C136	0.9
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.9
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	0.9
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	0.9
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	0.9
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	0.9
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	0.9
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	0.9
LDTP05859	Integrin-linked protein kinase (ILK)				C346	0.9
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	0.8
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	0.8
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.8
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	0.8
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.8
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	0.8
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	0.8
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.8
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.8
LDTP10774	Elongation factor G, mitochondrial (GFM1)				C153	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	20.0
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.3
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.2
LDTP04801	Gasdermin-D (GSDMD)				C268	1.1
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.1
LDTP04662	Exportin-2 (CSE1L)				C842	1.0
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.0
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.0
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.0
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	1.0
LDTP01574	Importin-7 (IPO7)				C757	1.0
LDTP00501	Exportin-1 (XPO1)				C34	0.8
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	0.8
LDTP13661	Sorting nexin-6 (SNX6)				C264	0.8
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	2.6
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.3
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.1
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.1
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.1
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.0
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	0.9
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	0.9
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.5
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.5
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.5
LDTP12412	Reticulon-4 (RTN4)				C1101	1.4
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	1.4
LDTP11718	Cleavage stimulation factor subunit 2 tau variant (CSTF2T)				C150	1.4
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	1.4
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1059	1.3
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.2
LDTP06330	Plectin (PLEC)				C992	1.2
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	1.2
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.2
LDTP04092	Crk-like protein (CRKL)				C249	1.2
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.2
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.2
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.2
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.2
LDTP05867	Treacle protein (TCOF1)				C38	1.2
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.1
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.1
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.1
LDTP14337	Protein strawberry notch homolog 1 (SBNO1)				C445	1.1
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.1
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.1
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.1
LDTP13088	Protein IMPACT (IMPACT)				C195	1.1
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.1
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.1
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	1.1
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.1
LDTP07755	Dynamin-binding protein (DNMBP)				C691	1.1
LDTP03620	Protein S100-A11 (S100A11)				C91	1.1
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	1.1
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.1
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	1.1
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.0
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.0
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	1.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	1.0
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.0
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.0
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.0
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.0
LDTP12443	Anillin (ANLN)				C712	1.0
LDTP10864	Calponin-2 (CNN2)				C164	1.0
LDTP04487	Cyclin-H (CCNH)				C244	1.0
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.0
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	1.0
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	1.0
LDTP04363	Serpin H1 (SERPINH1)				C156	1.0
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.0
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.0
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.0
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.0
LDTP10864	Calponin-2 (CNN2)				C215	1.0
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.0
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.0
LDTP13580	Coronin-1C (CORO1C)				C420	1.0
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.0
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.0
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.0
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.0
LDTP08885	Actin filament-associated protein 1 (AFAP1)				C713	1.0
LDTP12914	Hsp70-binding protein 1 (HSPBP1)				C204	1.0
LDTP06681	Inverted formin-2 (INF2)				C971	1.0
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	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
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.0
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	0.9
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	0.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	0.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	0.9
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	0.9
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	0.9
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	0.9
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	0.9
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	0.9
LDTP06330	Plectin (PLEC)				C3110	0.9
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	0.9
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	0.9
LDTP08238	Kinectin (KTN1)				C303	0.9
LDTP00202	AH receptor-interacting protein (AIP)				C122	0.9
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	0.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	0.9
LDTP11235	Protein PAXX (PAXX)				C180	0.9
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	0.9
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.9
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	0.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	0.9
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	0.9
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	0.9
LDTP05867	Treacle protein (TCOF1)				C1298	0.9
LDTP02692	Plastin-3 (PLS3)				C33	0.9
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	0.9
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.8
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	0.8
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	0.8
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	0.8
LDTP13580	Coronin-1C (CORO1C)				C456	0.8
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	0.8
LDTP03244	Cofilin-1 (CFL1)				C80	0.8
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	0.8
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	0.8
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	0.8
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	0.7

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.