Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment23					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
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	20.0
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	7.4
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	7.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	6.1
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	5.6
LDTP03496	Protein PML (PML)				C389	5.5
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	5.0
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	3.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	3.6
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	3.5
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	3.4
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	3.1
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	3.1
LDTP02198	Cathepsin D (CTSD)				C117	3.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	3.1
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	2.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	2.9
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	2.9
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	2.9
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	2.8
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	2.8
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	2.6
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	2.5
LDTP02223	Cathepsin B (CTSB)				C211	2.3
LDTP02502	Thioredoxin (TXN)				C32	2.3
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	2.1
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	2.0
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.9
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.9
LDTP02223	Cathepsin B (CTSB)				C319	1.9
LDTP13147	Cathepsin Z (CTSZ)				C173	1.8
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.8
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.8
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.7
LDTP04374	Dynamin-2 (DNM2)				C27	1.7
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.6
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.6
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.6
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.6
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	1.6
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.6
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.5
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.5
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	1.5
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.5
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.5
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.5
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.4
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.4
LDTP06211	Caspase-8 (CASP8)				C360	1.4
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.4
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.4
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	1.4
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.3
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.3
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.3
LDTP02672	Elongation factor 2 (EEF2)				C41	1.2
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.1
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.1
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.1
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	1.1
LDTP05289	AMP deaminase 2 (AMPD2)				C107	1.1
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.0
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.0
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	1.0
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.0
LDTP02672	Elongation factor 2 (EEF2)				C136	1.0
LDTP13147	Cathepsin Z (CTSZ)				C92	1.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.0
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.0
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.0
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	1.0
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.0
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.0
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	0.9
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	0.9
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	0.9
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	0.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	0.9
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	0.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	0.9
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.9
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.9
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	0.8
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.8
LDTP13080	GMP reductase 2 (GMPR2)				C186	0.8
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	0.8
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	0.8
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	0.8
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	0.8
LDTP02733	Pyruvate kinase PKM (PKM)				C423	0.8
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	0.8
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.7
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.7
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	0.7
LDTP03642	Cytidine deaminase (CDA)				C14	0.6
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.6
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	0.6
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	0.6
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	0.6
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	0.5
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.4
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.3

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	4.6
LDTP00501	Exportin-1 (XPO1)				C34	3.4
LDTP01574	Importin-7 (IPO7)				C757	3.1
LDTP13661	Sorting nexin-6 (SNX6)				C264	3.0
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	2.2
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.8
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.4
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	1.2
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.2
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.1
LDTP04801	Gasdermin-D (GSDMD)				C268	1.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.8
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	0.8
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.7
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	20.0
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	9.6
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	7.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.3
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.2
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	0.8
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03244	Cofilin-1 (CFL1)				C80	20.0
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	20.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	20.0
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	20.0
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	12.5
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	9.4
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	8.2
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	5.2
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	5.0
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	4.0
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	3.6
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	3.5
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	3.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	3.2
LDTP13925	Nucleolar protein 58 (NOP58)				C106	3.2
LDTP13580	Coronin-1C (CORO1C)				C456	3.2
LDTP12412	Reticulon-4 (RTN4)				C1101	3.2
LDTP02205	Tubulin beta chain (TUBB)				C354	2.9
LDTP02205	Tubulin beta chain (TUBB)				C239	2.8
LDTP06330	Plectin (PLEC)				C992	2.7
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	2.7
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	2.6
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	2.6
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	2.5
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	2.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	2.4
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	2.4
LDTP05867	Treacle protein (TCOF1)				C1298	2.4
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	2.3
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	2.1
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	2.0
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	2.0
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	1.9
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.9
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	1.9
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.9
LDTP10864	Calponin-2 (CNN2)				C215	1.8
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.8
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.6
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.6
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.6
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.6
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.5
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.5
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.4
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.4
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.4
LDTP12443	Anillin (ANLN)				C712	1.3
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.3
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.3
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.3
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.3
LDTP06330	Plectin (PLEC)				C3110	1.3
LDTP05867	Treacle protein (TCOF1)				C38	1.2
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.2
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.2
LDTP13580	Coronin-1C (CORO1C)				C420	1.2
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.2
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.1
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.1
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.1
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.1
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.1
LDTP06681	Inverted formin-2 (INF2)				C971	1.0
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.0
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.0
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	1.0
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.0
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.0
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.9
LDTP04363	Serpin H1 (SERPINH1)				C156	0.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	0.9
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	0.9
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	0.9
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	0.9
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.9
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	0.9
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	0.8
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	0.8
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	0.8
LDTP02692	Plastin-3 (PLS3)				C33	0.8
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	0.7
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	0.7
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	0.7
LDTP04092	Crk-like protein (CRKL)				C249	0.7
LDTP00202	AH receptor-interacting protein (AIP)				C122	0.7
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	0.5
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	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.