Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment52					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
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	6.8
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	4.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	3.8
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	2.7
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	2.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.9
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.7
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.6
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.6
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	1.6
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.5
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.5
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.5
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	1.5
LDTP02693	Acylamino-acid-releasing enzyme (APEH)				C641	1.5
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.5
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.5
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.4
LDTP07110	Putative transferase CAF17, mitochondrial (IBA57)				C170	1.4
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.3
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.3
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.3
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.3
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.3
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.3
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.3
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.3
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.3
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.2
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.2
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.2
LDTP04424	Galactokinase (GALK1)				C182	1.2
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.2
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.2
LDTP02672	Elongation factor 2 (EEF2)				C41	1.2
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.2
LDTP04689	Adenosine kinase (ADK)				C353	1.2
LDTP02223	Cathepsin B (CTSB)				C319	1.2
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.2
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.2
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.1
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.1
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.1
LDTP05289	AMP deaminase 2 (AMPD2)				C107	1.1
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.1
LDTP02198	Cathepsin D (CTSD)				C117	1.1
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.1
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.1
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.1
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.1
LDTP03496	Protein PML (PML)				C389	1.1
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.1
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.1
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.1
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.1
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.1
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.1
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.1
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	1.1
LDTP04374	Dynamin-2 (DNM2)				C27	1.1
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.0
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP02502	Thioredoxin (TXN)				C32	1.0
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.0
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.0
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.0
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.0
LDTP03642	Cytidine deaminase (CDA)				C14	1.0
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.0
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.0
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.0
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.0
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.9
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	0.9
LDTP13147	Cathepsin Z (CTSZ)				C92	0.9
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.9
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	0.9
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	0.9
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	0.9
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.8
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	0.8
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	0.8
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	0.8
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.8
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	0.8
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	0.7
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	0.7
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.7
LDTP14036	Helicase ARIP4 (RAD54L2)				C820	0.7
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	0.5

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	2.4
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.4
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.3
LDTP00501	Exportin-1 (XPO1)				C528	1.3
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.2
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.1
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.1
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.1
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.1
LDTP00501	Exportin-1 (XPO1)				C34	1.0
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.0
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.0
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.0
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	1.1
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	1.0
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.0
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.0
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	0.9
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	0.9
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	0.9
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03997	Leucine-rich PPR motif-containing protein, mitochondrial (LRPPRC)				C500	20.0
LDTP06330	Plectin (PLEC)				C4071	2.0
LDTP05867	Treacle protein (TCOF1)				C38	1.9
LDTP13925	Nucleolar protein 58 (NOP58)				C106	1.9
LDTP09549	Conserved oligomeric Golgi complex subunit 1 (COG1)				C513	1.8
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.8
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.8
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.8
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.7
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.6
LDTP04363	Serpin H1 (SERPINH1)				C156	1.6
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.6
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.6
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.5
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.5
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.5
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.5
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.5
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.4
LDTP05867	Treacle protein (TCOF1)				C1298	1.4
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.4
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.4
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.4
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.4
LDTP12443	Anillin (ANLN)				C712	1.3
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.3
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	1.3
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.3
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	1.3
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.3
LDTP01532	ZW10 interactor (ZWINT)				C54	1.3
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.3
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.3
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.2
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.2
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	1.2
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.2
LDTP10864	Calponin-2 (CNN2)				C164	1.2
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.2
LDTP06330	Plectin (PLEC)				C3110	1.2
LDTP02205	Tubulin beta chain (TUBB)				C354	1.2
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.2
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.2
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.2
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	1.2
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.2
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.2
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.2
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.2
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.2
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.1
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.1
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.1
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.1
LDTP02205	Tubulin beta chain (TUBB)				C239	1.1
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	1.1
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C767	1.1
LDTP02692	Plastin-3 (PLS3)				C33	1.1
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.1
LDTP13580	Coronin-1C (CORO1C)				C420	1.1
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.1
LDTP04487	Cyclin-H (CCNH)				C244	1.0
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.0
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	1.0
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.0
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.0
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.0
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.0
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.0
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.0
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.0
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.0
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.0
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	1.0
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.0
LDTP04092	Crk-like protein (CRKL)				C249	1.0
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.0
LDTP13580	Coronin-1C (CORO1C)				C456	1.0
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.0
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	0.9
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.9
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	0.9
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	0.9
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	0.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	0.9
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	0.9
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	0.9
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	0.8
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	0.7
LDTP03620	Protein S100-A11 (S100A11)				C91	0.7
LDTP03244	Cofilin-1 (CFL1)				C80	0.7
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.5
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.3

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.