Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment11					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
LDTP05992	Bleomycin hydrolase (BLMH)				C73	20.0
LDTP06211	Caspase-8 (CASP8)				C360	20.0
LDTP06603	Cyclin-dependent kinase inhibitor 3 (CDKN3)				C39	20.0
LDTP03642	Cytidine deaminase (CDA)				C14	20.0
LDTP03681	DNA replication licensing factor MCM5 (MCM5)				C482	20.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	20.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	20.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	20.0
LDTP05859	Integrin-linked protein kinase (ILK)				C346	20.0
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	20.0
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	20.0
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	20.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	20.0
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	20.0
LDTP07098	Probable ATP-dependent RNA helicase DDX59 (DDX59)				C453	20.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	20.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	20.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	20.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	20.0
LDTP15484	Saccharopine dehydrogenase-like oxidoreductase (SCCPDH)				C238	20.0
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	20.0
LDTP09412	Serine/threonine-protein kinase Nek9 (NEK9)				C623	20.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	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
LDTP14159	Ubiquitin carboxyl-terminal hydrolase 16 (USP16)				C205	20.0
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	20.0
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	20.0
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	19.1
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	10.5
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	7.7
LDTP02198	Cathepsin D (CTSD)				C117	6.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	6.4
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	6.1
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	5.9
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	5.0
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	4.9
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	4.9
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	4.8
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	4.6
LDTP13147	Cathepsin Z (CTSZ)				C92	4.6
LDTP13147	Cathepsin Z (CTSZ)				C173	4.6
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	3.5
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	3.4
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	3.3
LDTP03400	Deoxycytidine kinase (DCK)				C9	3.2
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	2.9
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	2.8
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	2.7
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	2.5
LDTP02223	Cathepsin B (CTSB)				C211	2.5
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	2.4
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	2.4
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	2.3
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	2.3
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	2.2
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	2.2
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	2.1
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	2.1
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	2.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	2.0
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	2.0
LDTP02672	Elongation factor 2 (EEF2)				C136	2.0
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	2.0
LDTP02223	Cathepsin B (CTSB)				C319	2.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.9
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.8
LDTP02672	Elongation factor 2 (EEF2)				C41	1.8
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.8
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.7
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.7
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.7
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.7
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.7
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.6
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.6
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	1.6
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.5
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	1.5
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.5
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.5
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.4
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.3
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	1.3
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.2
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.2
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.2
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.2
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.1
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	1.1
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.1
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.1
LDTP04689	Adenosine kinase (ADK)				C353	1.0
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.0
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP04374	Dynamin-2 (DNM2)				C27	1.0
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.0
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.0
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	0.9
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.8
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.8
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.6

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
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	20.0
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	20.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	20.0
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	2.3
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	1.9
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.6
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.5
LDTP04662	Exportin-2 (CSE1L)				C842	1.3
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.2
LDTP00501	Exportin-1 (XPO1)				C34	1.2
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.1
LDTP01574	Importin-7 (IPO7)				C757	1.0
LDTP00501	Exportin-1 (XPO1)				C528	1.0
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.0

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	20.0
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	20.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	20.0
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	9.4
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	5.8
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.7
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.2
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	20.0
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	20.0
LDTP06681	Inverted formin-2 (INF2)				C971	20.0
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	20.0
LDTP02692	Plastin-3 (PLS3)				C33	20.0
LDTP13088	Protein IMPACT (IMPACT)				C195	20.0
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	20.0
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	20.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	20.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	15.4
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	15.3
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	9.9
LDTP12443	Anillin (ANLN)				C712	7.1
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	4.8
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	4.6
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	4.6
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	4.3
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	4.2
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	3.3
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	3.3
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	3.3
LDTP01532	ZW10 interactor (ZWINT)				C54	3.3
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	3.2
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	3.2
LDTP05867	Treacle protein (TCOF1)				C1298	3.1
LDTP13580	Coronin-1C (CORO1C)				C420	3.0
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	3.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	3.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	2.9
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	2.9
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	2.8
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	2.7
LDTP10864	Calponin-2 (CNN2)				C164	2.6
LDTP13925	Nucleolar protein 58 (NOP58)				C106	2.6
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	2.6
LDTP05867	Treacle protein (TCOF1)				C38	2.5
LDTP06330	Plectin (PLEC)				C4071	2.4
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	2.4
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	2.3
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	2.3
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	2.3
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	2.3
LDTP02205	Tubulin beta chain (TUBB)				C354	2.2
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	2.2
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	2.1
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	2.1
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	2.0
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	2.0
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	2.0
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	2.0
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.9
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.9
LDTP06330	Plectin (PLEC)				C992	1.9
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.8
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.8
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.8
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.8
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.7
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.7
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	1.7
LDTP06330	Plectin (PLEC)				C3110	1.7
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.6
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.5
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.5
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.4
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.4
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.4
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.4
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.4
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.3
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.3
LDTP04487	Cyclin-H (CCNH)				C244	1.3
LDTP04518	DNA mismatch repair protein Msh6 (MSH6)				C1117	1.2
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.2
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.2
LDTP02205	Tubulin beta chain (TUBB)				C239	1.2
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.2
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.2
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.2
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.2
LDTP03620	Protein S100-A11 (S100A11)				C91	1.2
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.1
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	1.1
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.1
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.1
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.1
LDTP08238	Kinectin (KTN1)				C303	1.1
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.1
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.1
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.0
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.0
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.0
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.0
LDTP03244	Cofilin-1 (CFL1)				C80	0.9
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.8
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	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.