Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment31					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
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	20.0
LDTP09912	DNA repair protein RAD50 (RAD50)				C102	13.0
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	7.9
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	6.1
LDTP03642	Cytidine deaminase (CDA)				C14	6.0
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	4.6
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	4.3
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	3.8
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	3.7
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	3.6
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	3.6
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	3.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	3.1
LDTP11931	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1)				C772	3.0
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	3.0
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	2.9
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	2.8
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	2.8
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	2.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	2.5
LDTP04689	Adenosine kinase (ADK)				C353	2.5
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	2.5
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	2.3
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	2.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	2.2
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	2.2
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	2.2
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	2.2
LDTP04374	Dynamin-2 (DNM2)				C27	2.2
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	2.2
LDTP02672	Elongation factor 2 (EEF2)				C41	2.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	2.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	2.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	2.1
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	2.1
LDTP03400	Deoxycytidine kinase (DCK)				C9	2.1
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	2.1
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	2.0
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	1.9
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	1.8
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.7
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.7
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	1.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.7
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.7
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.6
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.6
LDTP05289	AMP deaminase 2 (AMPD2)				C107	1.6
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.6
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.6
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.6
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.6
LDTP02223	Cathepsin B (CTSB)				C319	1.5
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	1.5
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.4
LDTP02223	Cathepsin B (CTSB)				C211	1.4
LDTP02502	Thioredoxin (TXN)				C32	1.4
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.4
LDTP13147	Cathepsin Z (CTSZ)				C173	1.4
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.4
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.3
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.3
LDTP02198	Cathepsin D (CTSD)				C117	1.3
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.3
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.3
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.3
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.3
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.3
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.3
LDTP10982	Aconitate hydratase, mitochondrial (ACO2)				C385	1.3
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.3
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.2
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.2
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.2
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.2
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.2
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.2
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	1.2
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.2
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	1.2
LDTP13147	Cathepsin Z (CTSZ)				C92	1.2
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.2
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.2
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.2
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	1.2
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.1
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.1
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.1
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.1
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	1.1
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.1
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.1
LDTP02672	Elongation factor 2 (EEF2)				C136	1.1
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.1
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.1
LDTP02693	Acylamino-acid-releasing enzyme (APEH)				C641	1.1
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	1.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.0
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.0
LDTP04253	Alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1)				C522	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.9
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	0.9
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	0.9
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.8
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.8
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.8
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	0.8
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.4

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP00501	Exportin-1 (XPO1)				C528	5.2
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	3.2
LDTP04662	Exportin-2 (CSE1L)				C842	3.1
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	2.8
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	2.5
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	1.6
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.4
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.3
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.1
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.1
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.1
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP00501	Exportin-1 (XPO1)				C34	1.0
LDTP01574	Importin-7 (IPO7)				C757	1.0

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	10.8
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	2.7
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	1.5
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.4
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.2
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.2
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.1

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	20.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	20.0
LDTP12412	Reticulon-4 (RTN4)				C1101	20.0
LDTP13925	Nucleolar protein 58 (NOP58)				C106	12.8
LDTP06681	Inverted formin-2 (INF2)				C332	10.8
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	10.3
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	5.9
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	4.4
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	4.1
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	3.5
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	3.1
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	2.7
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	2.6
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	2.6
LDTP06681	Inverted formin-2 (INF2)				C971	2.5
LDTP02205	Tubulin beta chain (TUBB)				C354	2.4
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	2.4
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	2.3
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	2.3
LDTP05233	55 kDa erythrocyte membrane protein (MPP1)				C179	2.3
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	2.3
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	2.3
LDTP04363	Serpin H1 (SERPINH1)				C156	2.2
LDTP02205	Tubulin beta chain (TUBB)				C239	2.2
LDTP14195	FH1/FH2 domain-containing protein 1 (FHOD1)				C502	2.1
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	2.0
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	2.0
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	2.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	2.0
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.9
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.9
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.9
LDTP04092	Crk-like protein (CRKL)				C249	1.8
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.8
LDTP13088	Protein IMPACT (IMPACT)				C195	1.8
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.8
LDTP03620	Protein S100-A11 (S100A11)				C91	1.8
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.7
LDTP05867	Treacle protein (TCOF1)				C38	1.7
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.7
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.7
LDTP04487	Cyclin-H (CCNH)				C244	1.7
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.7
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.7
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.7
LDTP10864	Calponin-2 (CNN2)				C215	1.7
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.7
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.7
LDTP12443	Anillin (ANLN)				C712	1.6
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.6
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.6
LDTP13580	Coronin-1C (CORO1C)				C420	1.6
LDTP01567	Structural maintenance of chromosomes protein 2 (SMC2)				C1174	1.6
LDTP06330	Plectin (PLEC)				C3110	1.5
LDTP08573	Ankyrin repeat and KH domain-containing protein 1 (ANKHD1)				C615	1.5
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	1.5
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.5
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.5
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.5
LDTP10864	Calponin-2 (CNN2)				C164	1.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.5
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.4
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.4
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.4
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.4
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.4
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.4
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.4
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.4
LDTP08238	Kinectin (KTN1)				C303	1.4
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.4
LDTP08885	Actin filament-associated protein 1 (AFAP1)				C713	1.3
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.3
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.3
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.3
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.3
LDTP04518	DNA mismatch repair protein Msh6 (MSH6)				C1117	1.2
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.2
LDTP13580	Coronin-1C (CORO1C)				C456	1.2
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.2
LDTP02692	Plastin-3 (PLS3)				C33	1.2
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.2
LDTP11235	Protein PAXX (PAXX)				C180	1.2
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.2
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.2
LDTP06330	Plectin (PLEC)				C992	1.2
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.2
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.2
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.2
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.1
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.1
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.1
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.1
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.0
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.0
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.0
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.0
LDTP03244	Cofilin-1 (CFL1)				C80	1.0
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.0
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	0.9

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.