Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment10					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
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	20.0
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	20.0
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	20.0
LDTP03400	Deoxycytidine kinase (DCK)				C9	20.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	20.0
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	20.0
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	20.0
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	20.0
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	20.0
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	20.0
LDTP12190	NmrA-like family domain-containing protein 1 (NMRAL1)				C154	20.0
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	20.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	20.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	20.0
LDTP02502	Thioredoxin (TXN)				C32	20.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	20.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	20.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	13.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	13.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	13.0
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	10.2
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	8.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	7.5
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	7.2
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	5.1
LDTP13080	GMP reductase 2 (GMPR2)				C186	5.0
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	4.9
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	4.6
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	4.5
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	4.1
LDTP02223	Cathepsin B (CTSB)				C211	3.8
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	3.7
LDTP03786	Glutaredoxin-1 (GLRX)				C23	3.6
LDTP05859	Integrin-linked protein kinase (ILK)				C346	3.5
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	3.5
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	3.4
LDTP02223	Cathepsin B (CTSB)				C319	3.4
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	3.4
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	3.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	3.2
LDTP13147	Cathepsin Z (CTSZ)				C92	3.1
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	3.0
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	2.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	2.9
LDTP03681	DNA replication licensing factor MCM5 (MCM5)				C482	2.8
LDTP06211	Caspase-8 (CASP8)				C360	2.8
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	2.8
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	2.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	2.7
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	2.7
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	2.6
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	2.6
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	2.5
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	2.5
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	2.5
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	2.5
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	2.4
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	2.4
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	2.4
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	2.3
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	2.3
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	2.3
LDTP04424	Galactokinase (GALK1)				C182	2.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	2.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	2.2
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	2.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	2.1
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	2.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.9
LDTP02672	Elongation factor 2 (EEF2)				C41	1.9
LDTP01495	E3 ubiquitin-protein ligase UBR5 (UBR5)				C2267	1.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.8
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.7
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.7
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.7
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.7
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.7
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.6
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.5
LDTP03496	Protein PML (PML)				C389	1.5
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.5
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.5
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.5
LDTP04689	Adenosine kinase (ADK)				C353	1.5
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.5
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.4
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.4
LDTP04374	Dynamin-2 (DNM2)				C27	1.3
LDTP02672	Elongation factor 2 (EEF2)				C136	1.3
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	1.3
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.2
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.2
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.2
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.1
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.1
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.1
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.0
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	0.9
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.9
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.5

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	10.6
LDTP04801	Gasdermin-D (GSDMD)				C268	7.0
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	3.7
LDTP04707	Protein SEC13 homolog (SEC13)				C187	2.5
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	2.3
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.7
LDTP04662	Exportin-2 (CSE1L)				C842	1.5
LDTP01574	Importin-7 (IPO7)				C757	1.3
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.3
LDTP00501	Exportin-1 (XPO1)				C34	1.2
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.2
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.1
LDTP00501	Exportin-1 (XPO1)				C528	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	20.0
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	4.4
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	4.2
LDTP02016	Glucocorticoid receptor (NR3C1)				C302	4.1
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.8
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	1.5
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.2
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.1

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	20.0
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	17.5
LDTP12412	Reticulon-4 (RTN4)				C1101	11.9
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	10.5
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	5.3
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	5.2
LDTP03620	Protein S100-A11 (S100A11)				C91	4.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	4.7
LDTP10864	Calponin-2 (CNN2)				C215	4.5
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	4.4
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	4.4
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	4.4
LDTP05233	55 kDa erythrocyte membrane protein (MPP1)				C179	4.2
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	3.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	3.8
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	3.6
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	3.6
LDTP04363	Serpin H1 (SERPINH1)				C156	3.4
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	3.3
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	3.2
LDTP12443	Anillin (ANLN)				C712	3.0
LDTP14337	Protein strawberry notch homolog 1 (SBNO1)				C445	3.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	2.9
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	2.9
LDTP18494	Tropomodulin-3 (TMOD3)				C132	2.9
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	2.9
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	2.8
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	2.8
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	2.7
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	2.7
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	2.7
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	2.7
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	2.6
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	2.6
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	2.6
LDTP10864	Calponin-2 (CNN2)				C164	2.6
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	2.5
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	2.4
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	2.4
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	2.4
LDTP06681	Inverted formin-2 (INF2)				C332	2.3
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	2.3
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	2.2
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	2.2
LDTP13580	Coronin-1C (CORO1C)				C420	2.1
LDTP06330	Plectin (PLEC)				C992	2.1
LDTP05867	Treacle protein (TCOF1)				C38	2.0
LDTP05867	Treacle protein (TCOF1)				C1298	2.0
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	2.0
LDTP13964	MOB-like protein phocein (MOB4)				C134	2.0
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	2.0
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.9
LDTP02205	Tubulin beta chain (TUBB)				C354	1.9
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.9
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.9
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.9
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.8
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.8
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.7
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.7
LDTP02205	Tubulin beta chain (TUBB)				C239	1.7
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.7
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.6
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.6
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.6
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.6
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.5
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.5
LDTP13088	Protein IMPACT (IMPACT)				C195	1.5
LDTP06330	Plectin (PLEC)				C3110	1.5
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.5
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	1.5
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1059	1.5
LDTP11235	Protein PAXX (PAXX)				C180	1.5
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.5
LDTP04487	Cyclin-H (CCNH)				C244	1.4
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.4
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.4
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.4
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.4
LDTP02692	Plastin-3 (PLS3)				C33	1.3
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	1.3
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.3
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.3
LDTP13580	Coronin-1C (CORO1C)				C456	1.3
LDTP08238	Kinectin (KTN1)				C303	1.3
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.2
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.1
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.1
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.1
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.1
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.1
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.0
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.0
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.0
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.0
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.8
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	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.