Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment47					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
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	3.3
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	2.5
LDTP03496	Protein PML (PML)				C389	2.2
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	2.0
LDTP03642	Cytidine deaminase (CDA)				C14	2.0
LDTP02198	Cathepsin D (CTSD)				C117	1.9
LDTP02223	Cathepsin B (CTSB)				C211	1.8
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.7
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.6
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.5
LDTP11111	Tudor-interacting repair regulator protein (NUDT16L1)				C88	1.5
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.4
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.4
LDTP04689	Adenosine kinase (ADK)				C353	1.4
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.4
LDTP04374	Dynamin-2 (DNM2)				C27	1.4
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.4
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	1.4
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.4
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.3
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.3
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.3
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.3
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.3
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	1.3
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.3
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.3
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.3
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	1.2
LDTP02223	Cathepsin B (CTSB)				C319	1.2
LDTP02672	Elongation factor 2 (EEF2)				C41	1.2
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.2
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.2
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.2
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.2
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.2
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.2
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.2
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.2
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.2
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	1.2
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.2
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.2
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.2
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	1.2
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	1.2
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.1
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.1
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.1
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.1
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.1
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.1
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.1
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.1
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	1.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.1
LDTP02502	Thioredoxin (TXN)				C32	1.1
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.0
LDTP07317	Tensin-3 (TNS3)				C888	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.0
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.0
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	1.0
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	0.9
LDTP13147	Cathepsin Z (CTSZ)				C92	0.9
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	0.9
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	0.9
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	0.9
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	0.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	0.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.9
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	0.9
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	0.9
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	0.9
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	0.9
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	0.9
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.9
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.9
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	0.8
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.7
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.7
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	0.7
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	0.7
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP00501	Exportin-1 (XPO1)				C528	2.2
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.6
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.4
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.3
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.2
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.1
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.1
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.1
LDTP00501	Exportin-1 (XPO1)				C34	1.0
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.0
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP04662	Exportin-2 (CSE1L)				C842	0.9
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	0.9
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.9
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	3.5
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	3.1
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.5
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	1.2
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.2
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.1
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.0

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	2.4
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.9
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.9
LDTP04487	Cyclin-H (CCNH)				C244	1.9
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.7
LDTP06330	Plectin (PLEC)				C992	1.6
LDTP13580	Coronin-1C (CORO1C)				C456	1.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.5
LDTP10864	Calponin-2 (CNN2)				C164	1.5
LDTP10864	Calponin-2 (CNN2)				C215	1.5
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	1.5
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.4
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	1.4
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.4
LDTP13580	Coronin-1C (CORO1C)				C420	1.4
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.4
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.4
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.4
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.4
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.4
LDTP12443	Anillin (ANLN)				C712	1.4
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	1.3
LDTP05867	Treacle protein (TCOF1)				C38	1.3
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.3
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.3
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.3
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.3
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.3
LDTP02205	Tubulin beta chain (TUBB)				C354	1.3
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.3
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.3
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.3
LDTP04363	Serpin H1 (SERPINH1)				C156	1.2
LDTP02205	Tubulin beta chain (TUBB)				C239	1.2
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.2
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.2
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.2
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.2
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.2
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.2
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.2
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.2
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.2
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.2
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.2
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.2
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.1
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	1.1
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.1
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.1
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.1
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.1
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.1
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.1
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	1.1
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.1
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.1
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.1
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.1
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	1.0
LDTP08885	Actin filament-associated protein 1 (AFAP1)				C713	1.0
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.0
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.0
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.0
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.0
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.0
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.0
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.0
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.0
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	1.0
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.0
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.0
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.0
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	0.9
LDTP13964	MOB-like protein phocein (MOB4)				C134	0.9
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	0.9
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.9
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.9
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	0.8
LDTP03620	Protein S100-A11 (S100A11)				C91	0.8
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.8
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	0.8
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	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.