Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment8					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
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	20.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	20.0
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	20.0
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	20.0
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	20.0
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	20.0
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	20.0
LDTP07098	Probable ATP-dependent RNA helicase DDX59 (DDX59)				C453	20.0
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	20.0
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	20.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	20.0
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	19.9
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	18.7
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	16.6
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	14.3
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	12.8
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	12.8
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	12.7
LDTP03786	Glutaredoxin-1 (GLRX)				C23	12.4
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	12.4
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	12.4
LDTP03642	Cytidine deaminase (CDA)				C14	12.1
LDTP05289	AMP deaminase 2 (AMPD2)				C107	12.1
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	11.1
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	11.0
LDTP02198	Cathepsin D (CTSD)				C117	6.2
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	5.9
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	5.8
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	5.7
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	5.5
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	5.1
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	4.7
LDTP09912	DNA repair protein RAD50 (RAD50)				C102	4.5
LDTP05859	Integrin-linked protein kinase (ILK)				C346	4.4
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	4.3
LDTP09598	Mitochondrial coenzyme A diphosphatase NUDT8 (NUDT8)				C207	4.1
LDTP02223	Cathepsin B (CTSB)				C211	3.9
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	3.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	3.7
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	3.4
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	3.3
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	3.2
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	3.2
LDTP13147	Cathepsin Z (CTSZ)				C92	3.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	3.0
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	2.8
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	2.8
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	2.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	2.7
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	2.6
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	2.6
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	2.6
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	2.5
LDTP02502	Thioredoxin (TXN)				C32	2.5
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	2.4
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	2.4
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	2.3
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	2.2
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	2.2
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	2.2
LDTP02672	Elongation factor 2 (EEF2)				C41	2.1
LDTP02223	Cathepsin B (CTSB)				C319	2.1
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	2.1
LDTP03496	Protein PML (PML)				C389	2.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	2.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	2.1
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	2.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	2.1
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	2.0
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	2.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	2.0
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	1.9
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.9
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.8
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.8
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.8
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.8
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	1.8
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.8
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.8
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.7
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.7
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.7
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.6
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.5
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.5
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.5
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.5
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.5
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.5
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.5
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	1.5
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.4
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.4
LDTP02672	Elongation factor 2 (EEF2)				C136	1.4
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.4
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.3
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.3
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.3
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.3
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.2
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.2
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.1
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.1
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.1
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.1
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.1
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	1.0
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.0
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.0
LDTP10982	Aconitate hydratase, mitochondrial (ACO2)				C385	1.0
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	1.0
LDTP04374	Dynamin-2 (DNM2)				C27	1.0
LDTP04689	Adenosine kinase (ADK)				C353	1.0
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.0
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.9
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.9
LDTP04253	Alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1)				C522	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.8
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.5

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	12.3
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	5.4
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	3.9
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	3.5
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	3.0
LDTP00501	Exportin-1 (XPO1)				C34	2.4
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	2.3
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	2.3
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	2.2
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.9
LDTP00501	Exportin-1 (XPO1)				C528	1.8
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.7
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.4
LDTP01574	Importin-7 (IPO7)				C757	1.3
LDTP04662	Exportin-2 (CSE1L)				C842	1.2
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.0
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	17.3
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	9.0
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	4.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	3.1
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	2.8
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.8
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.3
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.0

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP08573	Ankyrin repeat and KH domain-containing protein 1 (ANKHD1)				C615	20.0
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	20.0
LDTP06681	Inverted formin-2 (INF2)				C971	20.0
LDTP04092	Crk-like protein (CRKL)				C249	16.2
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C767	15.3
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	13.7
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	13.2
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	12.4
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	7.1
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	4.7
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	4.4
LDTP04363	Serpin H1 (SERPINH1)				C156	4.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	3.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	3.9
LDTP12443	Anillin (ANLN)				C712	3.8
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	3.8
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	3.7
LDTP10864	Calponin-2 (CNN2)				C164	3.6
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	3.5
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	3.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	3.5
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	3.3
LDTP10864	Calponin-2 (CNN2)				C215	3.3
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	3.3
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	3.1
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	3.1
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	3.0
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	2.8
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	2.7
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	2.7
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	2.7
LDTP13925	Nucleolar protein 58 (NOP58)				C106	2.6
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	2.6
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	2.6
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	2.6
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	2.5
LDTP05867	Treacle protein (TCOF1)				C1298	2.5
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	2.5
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	2.4
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	2.4
LDTP13580	Coronin-1C (CORO1C)				C420	2.4
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	2.3
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	2.2
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	2.2
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	2.2
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	2.1
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	2.1
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	2.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	2.0
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	2.0
LDTP05867	Treacle protein (TCOF1)				C38	2.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	2.0
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.9
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.9
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.9
LDTP02205	Tubulin beta chain (TUBB)				C354	1.8
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.8
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.8
LDTP06330	Plectin (PLEC)				C992	1.8
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.8
LDTP08238	Kinectin (KTN1)				C303	1.7
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.6
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.6
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.6
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.6
LDTP02692	Plastin-3 (PLS3)				C33	1.5
LDTP12412	Reticulon-4 (RTN4)				C1101	1.5
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.5
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.5
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.5
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.5
LDTP11235	Protein PAXX (PAXX)				C180	1.5
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.5
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.4
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.4
LDTP02205	Tubulin beta chain (TUBB)				C239	1.4
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.4
LDTP06330	Plectin (PLEC)				C3110	1.4
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.4
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.3
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.3
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.3
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.3
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.3
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.3
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.3
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.3
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.2
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.2
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.1
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.1
LDTP03620	Protein S100-A11 (S100A11)				C91	1.0
LDTP13580	Coronin-1C (CORO1C)				C456	1.0
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.0
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.0
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.9
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	0.9
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	0.9
LDTP04487	Cyclin-H (CCNH)				C244	0.8
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	0.8
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	0.8

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.