Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment13					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
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	15.6
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	9.6
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	7.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	5.5
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	5.2
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	4.9
LDTP02502	Thioredoxin (TXN)				C32	4.2
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	4.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	4.0
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	3.7
LDTP03642	Cytidine deaminase (CDA)				C14	3.0
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	2.8
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	2.7
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	2.6
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	2.3
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	2.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	2.2
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	2.2
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	2.1
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	2.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	2.1
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	2.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	2.0
LDTP10982	Aconitate hydratase, mitochondrial (ACO2)				C385	2.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.9
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.9
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.9
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	1.9
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.8
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	1.8
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.8
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.8
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.8
LDTP02223	Cathepsin B (CTSB)				C211	1.8
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.7
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	1.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.6
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	1.5
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.5
LDTP11931	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1)				C772	1.5
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.5
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.5
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.5
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.5
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	1.5
LDTP02672	Elongation factor 2 (EEF2)				C41	1.5
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	1.5
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	1.4
LDTP07317	Tensin-3 (TNS3)				C888	1.4
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.4
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	1.4
LDTP13147	Cathepsin Z (CTSZ)				C173	1.4
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.3
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	1.3
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.2
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.2
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.2
LDTP02223	Cathepsin B (CTSB)				C319	1.2
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.2
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	1.2
LDTP03496	Protein PML (PML)				C389	1.2
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.2
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.2
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.1
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.1
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.1
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.1
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.1
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.1
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.1
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.1
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.1
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.1
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.1
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.1
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.1
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.1
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.0
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.0
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	1.0
LDTP04374	Dynamin-2 (DNM2)				C27	1.0
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.0
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.0
LDTP02672	Elongation factor 2 (EEF2)				C136	1.0
LDTP04689	Adenosine kinase (ADK)				C353	1.0
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.0
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	0.9
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	0.9
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.9
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	0.9
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.9
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	0.9
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.9
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	0.9
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.8
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	0.8
LDTP04253	Alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1)				C522	0.7
LDTP04424	Galactokinase (GALK1)				C182	0.2

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	20.0
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	9.2
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	2.5
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.9
LDTP04801	Gasdermin-D (GSDMD)				C268	1.8
LDTP04662	Exportin-2 (CSE1L)				C842	1.6
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.4
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.4
LDTP01574	Importin-7 (IPO7)				C757	1.2
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.2
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	1.1
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.0
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.0
LDTP13661	Sorting nexin-6 (SNX6)				C264	0.9
LDTP00501	Exportin-1 (XPO1)				C34	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	2.2
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.3
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.0
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12412	Reticulon-4 (RTN4)				C1101	3.9
LDTP07755	Dynamin-binding protein (DNMBP)				C691	2.3
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	2.1
LDTP04092	Crk-like protein (CRKL)				C249	2.0
LDTP12914	Hsp70-binding protein 1 (HSPBP1)				C204	2.0
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	2.0
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.7
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	1.7
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.6
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.6
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.6
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.5
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.5
LDTP10864	Calponin-2 (CNN2)				C164	1.5
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.5
LDTP11235	Protein PAXX (PAXX)				C180	1.5
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.5
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.5
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.5
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	1.4
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.4
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.4
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	1.4
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.4
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	1.4
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.4
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.4
LDTP11212	Tubulin-specific chaperone D (TBCD)				C850	1.3
LDTP10864	Calponin-2 (CNN2)				C215	1.3
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.3
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.3
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.3
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.3
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.3
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.3
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.3
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.3
LDTP13580	Coronin-1C (CORO1C)				C420	1.2
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.2
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.2
LDTP02692	Plastin-3 (PLS3)				C33	1.1
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.1
LDTP02205	Tubulin beta chain (TUBB)				C239	1.1
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.1
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.1
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.1
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	1.1
LDTP13591	A-kinase anchor protein 8-like (AKAP8L)				C211	1.1
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.1
LDTP06330	Plectin (PLEC)				C992	1.1
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	1.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.0
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.0
LDTP02205	Tubulin beta chain (TUBB)				C354	1.0
LDTP09549	Conserved oligomeric Golgi complex subunit 1 (COG1)				C513	1.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.0
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.0
LDTP08238	Kinectin (KTN1)				C303	1.0
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.0
LDTP03620	Protein S100-A11 (S100A11)				C91	1.0
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.0
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	0.9
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	0.9
LDTP04363	Serpin H1 (SERPINH1)				C156	0.9
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	0.9
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	0.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	0.9
LDTP13580	Coronin-1C (CORO1C)				C456	0.9
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.9
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	0.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	0.8
LDTP06330	Plectin (PLEC)				C4071	0.8
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	0.8
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	0.8
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	0.8
LDTP12443	Anillin (ANLN)				C712	0.8
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	0.8
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	0.8
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	0.8
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	0.8
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	0.8
LDTP06330	Plectin (PLEC)				C3110	0.7
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	0.7
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	0.7
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	0.7
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	0.7
LDTP11718	Cleavage stimulation factor subunit 2 tau variant (CSTF2T)				C150	0.7
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.6
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	0.6

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.