Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment41					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
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	9.8
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	8.7
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	5.1
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	4.5
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	3.7
LDTP09912	DNA repair protein RAD50 (RAD50)				C102	3.2
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	2.9
LDTP03642	Cytidine deaminase (CDA)				C14	2.6
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	2.3
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	2.2
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	2.2
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.9
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.8
LDTP03496	Protein PML (PML)				C389	1.8
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.8
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.6
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	1.6
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.5
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.5
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.5
LDTP02672	Elongation factor 2 (EEF2)				C41	1.5
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	1.5
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.5
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.5
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.5
LDTP10774	Elongation factor G, mitochondrial (GFM1)				C153	1.5
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.4
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.4
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.4
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.4
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.3
LDTP02198	Cathepsin D (CTSD)				C117	1.3
LDTP12190	NmrA-like family domain-containing protein 1 (NMRAL1)				C154	1.3
LDTP07317	Tensin-3 (TNS3)				C888	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.3
LDTP04374	Dynamin-2 (DNM2)				C27	1.3
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.3
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	1.3
LDTP05289	AMP deaminase 2 (AMPD2)				C107	1.3
LDTP04689	Adenosine kinase (ADK)				C353	1.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.3
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.3
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.3
LDTP07098	Probable ATP-dependent RNA helicase DDX59 (DDX59)				C414	1.2
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.2
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.2
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.2
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.2
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	1.2
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.2
LDTP13147	Cathepsin Z (CTSZ)				C173	1.2
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.2
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.2
LDTP02223	Cathepsin B (CTSB)				C211	1.2
LDTP11111	Tudor-interacting repair regulator protein (NUDT16L1)				C88	1.2
LDTP02502	Thioredoxin (TXN)				C32	1.1
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.1
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.1
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.1
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.1
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.1
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.1
LDTP02223	Cathepsin B (CTSB)				C319	1.1
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.1
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.1
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	1.1
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.1
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.0
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	1.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.0
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.0
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	1.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	1.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.0
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.0
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.0
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.0
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.0
LDTP06211	Caspase-8 (CASP8)				C360	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	1.0
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	0.9
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	0.9
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	0.9
LDTP13147	Cathepsin Z (CTSZ)				C92	0.9
LDTP02672	Elongation factor 2 (EEF2)				C136	0.9
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	0.9
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.9
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	0.9
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	0.8
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	0.8
LDTP14159	Ubiquitin carboxyl-terminal hydrolase 16 (USP16)				C205	0.8
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	0.8
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	0.8
LDTP04424	Galactokinase (GALK1)				C182	0.8
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.8
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.8
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.8
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	0.8
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.7
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	0.5
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	0.5
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.5

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP00501	Exportin-1 (XPO1)				C34	3.1
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	2.5
LDTP13661	Sorting nexin-6 (SNX6)				C264	2.0
LDTP04801	Gasdermin-D (GSDMD)				C268	1.6
LDTP04662	Exportin-2 (CSE1L)				C842	1.6
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.5
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.4
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.3
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.0
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.0
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	0.9
LDTP11855	Pinin (PNN)				C249	0.9
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.9
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	0.7
LDTP00501	Exportin-1 (XPO1)				C528	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	20.0
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	3.3
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.8
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.8
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.6
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.3
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	1.2

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	20.0
LDTP03620	Protein S100-A11 (S100A11)				C91	20.0
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	6.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	5.6
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	5.2
LDTP18494	Tropomodulin-3 (TMOD3)				C132	5.2
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	3.9
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	3.5
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	3.2
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	2.7
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	2.6
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	2.6
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	2.4
LDTP13964	MOB-like protein phocein (MOB4)				C134	2.3
LDTP11235	Protein PAXX (PAXX)				C180	2.2
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	2.1
LDTP05233	55 kDa erythrocyte membrane protein (MPP1)				C179	2.0
LDTP11718	Cleavage stimulation factor subunit 2 tau variant (CSTF2T)				C150	1.9
LDTP13580	Coronin-1C (CORO1C)				C456	1.8
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.7
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.7
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.6
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.6
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.6
LDTP05867	Treacle protein (TCOF1)				C38	1.6
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	1.6
LDTP05867	Treacle protein (TCOF1)				C1298	1.5
LDTP08885	Actin filament-associated protein 1 (AFAP1)				C713	1.5
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.5
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	1.5
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.5
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	1.5
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	1.4
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.4
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.4
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.4
LDTP07755	Dynamin-binding protein (DNMBP)				C691	1.4
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.4
LDTP13591	A-kinase anchor protein 8-like (AKAP8L)				C211	1.4
LDTP12412	Reticulon-4 (RTN4)				C1101	1.4
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.3
LDTP12443	Anillin (ANLN)				C712	1.3
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	1.3
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.3
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.3
LDTP04363	Serpin H1 (SERPINH1)				C156	1.3
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.3
LDTP06330	Plectin (PLEC)				C3110	1.3
LDTP06681	Inverted formin-2 (INF2)				C971	1.3
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.3
LDTP13580	Coronin-1C (CORO1C)				C420	1.3
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.3
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.2
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.2
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.2
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	1.2
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.2
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.2
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	1.2
LDTP10864	Calponin-2 (CNN2)				C215	1.2
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C767	1.2
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.2
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.2
LDTP10864	Calponin-2 (CNN2)				C164	1.2
LDTP01567	Structural maintenance of chromosomes protein 2 (SMC2)				C1174	1.2
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.2
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.1
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.1
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.1
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.1
LDTP04092	Crk-like protein (CRKL)				C249	1.1
LDTP00202	AH receptor-interacting protein (AIP)				C122	1.1
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.1
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.0
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.0
LDTP02692	Plastin-3 (PLS3)				C33	1.0
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.0
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	1.0
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	0.9
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	0.9
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	0.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	0.9
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	0.9
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.8
LDTP11890	Protein unc-45 homolog A (UNC45A)				C426	0.8
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	0.8
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.7
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	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.