Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment39					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
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	20.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	20.0
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	20.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	20.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	18.8
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	15.7
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	11.4
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	7.6
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	4.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	3.9
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	3.8
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	3.6
LDTP13080	GMP reductase 2 (GMPR2)				C186	3.6
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	3.2
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	3.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	3.1
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	3.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	3.0
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	2.8
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	2.7
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	2.6
LDTP05859	Integrin-linked protein kinase (ILK)				C346	2.5
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	2.4
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	2.2
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	2.0
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	2.0
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	2.0
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.9
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.9
LDTP02672	Elongation factor 2 (EEF2)				C41	1.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.8
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	1.8
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.8
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.7
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.7
LDTP02672	Elongation factor 2 (EEF2)				C136	1.6
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.6
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.5
LDTP13147	Cathepsin Z (CTSZ)				C92	1.5
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.5
LDTP13147	Cathepsin Z (CTSZ)				C173	1.5
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.4
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.4
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.4
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.4
LDTP04424	Galactokinase (GALK1)				C182	1.4
LDTP02198	Cathepsin D (CTSD)				C117	1.3
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.2
LDTP04689	Adenosine kinase (ADK)				C353	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.2
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.1
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.1
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.1
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.1
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.0
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP02502	Thioredoxin (TXN)				C32	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.9
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.9
LDTP02733	Pyruvate kinase PKM (PKM)				C423	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.8
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP04801	Gasdermin-D (GSDMD)				C268	20.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	3.2
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	2.5
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.9
LDTP00501	Exportin-1 (XPO1)				C34	1.3
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.0
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.0
LDTP01574	Importin-7 (IPO7)				C757	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	20.0
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	2.5
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.2
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.1

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	20.0
LDTP05867	Treacle protein (TCOF1)				C38	4.8
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	4.2
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	3.5
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	2.5
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	2.3
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	2.2
LDTP12443	Anillin (ANLN)				C712	2.1
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	2.1
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	2.0
LDTP03620	Protein S100-A11 (S100A11)				C91	2.0
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	2.0
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.8
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.8
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.7
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.7
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.7
LDTP02692	Plastin-3 (PLS3)				C33	1.6
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.5
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.5
LDTP02205	Tubulin beta chain (TUBB)				C354	1.5
LDTP10864	Calponin-2 (CNN2)				C164	1.5
LDTP02205	Tubulin beta chain (TUBB)				C239	1.5
LDTP10864	Calponin-2 (CNN2)				C215	1.4
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.4
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.4
LDTP13580	Coronin-1C (CORO1C)				C420	1.3
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.3
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.3
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.3
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.2
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.2
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.1
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.1
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.0
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.0
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	0.9
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.8
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	0.8
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.7
LDTP03244	Cofilin-1 (CFL1)				C80	0.7

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.