Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment43					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
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	20.0
LDTP02672	Elongation factor 2 (EEF2)				C136	20.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	20.0
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	20.0
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	20.0
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	20.0
LDTP07098	Probable ATP-dependent RNA helicase DDX59 (DDX59)				C453	20.0
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	20.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	20.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	20.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	20.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	20.0
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	20.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	20.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	20.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	18.5
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	16.5
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	15.9
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	14.5
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	13.9
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	12.3
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	9.6
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	6.4
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	6.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	5.7
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	5.4
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	4.9
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	4.8
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	4.1
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	4.1
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	4.1
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	3.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	3.6
LDTP05289	AMP deaminase 2 (AMPD2)				C107	3.5
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	3.5
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	3.4
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	3.2
LDTP09912	DNA repair protein RAD50 (RAD50)				C102	3.2
LDTP02198	Cathepsin D (CTSD)				C117	3.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	3.0
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	2.9
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	2.9
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	2.8
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	2.8
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	2.7
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	2.7
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	2.7
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	2.6
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	2.6
LDTP04424	Galactokinase (GALK1)				C182	2.5
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	2.4
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	2.4
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	2.4
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	2.3
LDTP14036	Helicase ARIP4 (RAD54L2)				C820	2.3
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	2.2
LDTP07317	Tensin-3 (TNS3)				C888	2.2
LDTP02502	Thioredoxin (TXN)				C32	2.1
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	2.1
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	2.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	2.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	2.0
LDTP13080	GMP reductase 2 (GMPR2)				C186	2.0
LDTP09412	Serine/threonine-protein kinase Nek9 (NEK9)				C623	1.9
LDTP02223	Cathepsin B (CTSB)				C211	1.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.8
LDTP02672	Elongation factor 2 (EEF2)				C41	1.7
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	1.7
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.6
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.6
LDTP03681	DNA replication licensing factor MCM5 (MCM5)				C482	1.6
LDTP02223	Cathepsin B (CTSB)				C319	1.5
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.4
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.4
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.4
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.4
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.4
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.3
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.3
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.3
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.3
LDTP03496	Protein PML (PML)				C389	1.1
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.1
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.1
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.1
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.0
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.0
LDTP10982	Aconitate hydratase, mitochondrial (ACO2)				C385	1.0
LDTP04689	Adenosine kinase (ADK)				C353	1.0
LDTP04374	Dynamin-2 (DNM2)				C27	1.0
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	0.9
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.9
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	0.9
LDTP02733	Pyruvate kinase PKM (PKM)				C423	0.9
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	0.8
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.8
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	20.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	20.0
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	12.4
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	8.6
LDTP00501	Exportin-1 (XPO1)				C528	4.6
LDTP13661	Sorting nexin-6 (SNX6)				C264	4.1
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	3.7
LDTP14808	Tumor necrosis factor alpha-induced protein 2 (TNFAIP2)				C45	3.0
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	3.0
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	2.9
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	2.0
LDTP04662	Exportin-2 (CSE1L)				C842	1.3
LDTP00501	Exportin-1 (XPO1)				C34	1.1
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.1
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	0.9
LDTP01574	Importin-7 (IPO7)				C757	0.9
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	20.0
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	20.0
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	20.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	20.0
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.9
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.8
LDTP02016	Glucocorticoid receptor (NR3C1)				C302	1.5
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.2
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.1

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP08573	Ankyrin repeat and KH domain-containing protein 1 (ANKHD1)				C615	20.0
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	20.0
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	20.0
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	20.0
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	20.0
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	20.0
LDTP02692	Plastin-3 (PLS3)				C33	20.0
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	20.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	20.0
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	20.0
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	13.0
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	6.4
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	5.8
LDTP12443	Anillin (ANLN)				C712	5.8
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	5.3
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	5.3
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	5.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	4.6
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	4.6
LDTP11235	Protein PAXX (PAXX)				C180	4.2
LDTP05867	Treacle protein (TCOF1)				C1298	4.0
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	3.8
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	3.6
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	3.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	3.0
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	2.9
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	2.9
LDTP01532	ZW10 interactor (ZWINT)				C54	2.8
LDTP13925	Nucleolar protein 58 (NOP58)				C106	2.6
LDTP05867	Treacle protein (TCOF1)				C38	2.6
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	2.5
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	2.5
LDTP06681	Inverted formin-2 (INF2)				C332	2.5
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	2.5
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	2.5
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	2.4
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	2.4
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	2.2
LDTP10864	Calponin-2 (CNN2)				C164	2.2
LDTP08238	Kinectin (KTN1)				C303	2.1
LDTP02205	Tubulin beta chain (TUBB)				C354	2.1
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	2.1
LDTP06330	Plectin (PLEC)				C4071	2.1
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	2.0
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	2.0
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	1.9
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.9
LDTP06330	Plectin (PLEC)				C3110	1.9
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	1.9
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.8
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.8
LDTP13580	Coronin-1C (CORO1C)				C420	1.8
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.7
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.7
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.7
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.6
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.6
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.5
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.5
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.5
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.5
LDTP02205	Tubulin beta chain (TUBB)				C239	1.5
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.5
LDTP03620	Protein S100-A11 (S100A11)				C91	1.5
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.5
LDTP11890	Protein unc-45 homolog A (UNC45A)				C426	1.4
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.4
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.4
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	1.3
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.3
LDTP06330	Plectin (PLEC)				C992	1.3
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.3
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.3
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.3
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.2
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.2
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.1
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.1
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.1
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.1
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.0
LDTP04487	Cyclin-H (CCNH)				C244	1.0
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.0
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.0
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.0
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.0
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	0.9
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.9
LDTP13580	Coronin-1C (CORO1C)				C456	0.9
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	0.8
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.8
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.7
LDTP04518	DNA mismatch repair protein Msh6 (MSH6)				C1117	0.7
LDTP03244	Cofilin-1 (CFL1)				C80	0.7
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.6
LDTP04092	Crk-like protein (CRKL)				C249	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.