Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment29					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
LDTP02223	Cathepsin B (CTSB)				C211	2.6
LDTP13147	Cathepsin Z (CTSZ)				C173	2.5
LDTP07110	Putative transferase CAF17, mitochondrial (IBA57)				C170	2.4
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	2.3
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	2.0
LDTP14036	Helicase ARIP4 (RAD54L2)				C820	1.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.9
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.8
LDTP02223	Cathepsin B (CTSB)				C319	1.7
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	1.7
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	1.7
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.6
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.6
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.6
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.6
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.5
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.5
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.5
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	1.5
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.5
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.5
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.4
LDTP02198	Cathepsin D (CTSD)				C117	1.4
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.4
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.4
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.4
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	1.3
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	1.3
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.3
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.3
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.3
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.3
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.3
LDTP05289	AMP deaminase 2 (AMPD2)				C107	1.3
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.3
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.3
LDTP04374	Dynamin-2 (DNM2)				C27	1.3
LDTP02502	Thioredoxin (TXN)				C32	1.3
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	1.3
LDTP02672	Elongation factor 2 (EEF2)				C41	1.3
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.3
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.2
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	1.2
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.2
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.2
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.2
LDTP03642	Cytidine deaminase (CDA)				C14	1.2
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.2
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.2
LDTP02672	Elongation factor 2 (EEF2)				C136	1.2
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	1.2
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.2
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.2
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	1.2
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.2
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.2
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.2
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	1.2
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.2
LDTP03496	Protein PML (PML)				C389	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.1
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.1
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.1
LDTP03681	DNA replication licensing factor MCM5 (MCM5)				C482	1.1
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.1
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.1
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.1
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	1.1
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.1
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.1
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.1
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.1
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	1.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.0
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.0
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.0
LDTP04689	Adenosine kinase (ADK)				C353	1.0
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.0
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.0
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.0
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.0
LDTP13147	Cathepsin Z (CTSZ)				C92	1.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.0
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.0
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.0
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	0.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.9
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	0.9
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.9
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	0.9
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	0.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	0.9
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	0.9
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	0.9
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.8
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	0.8
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.8
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	0.8
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	0.8
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	0.8
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	17.5
LDTP14808	Tumor necrosis factor alpha-induced protein 2 (TNFAIP2)				C45	1.5
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	1.5
LDTP00501	Exportin-1 (XPO1)				C34	1.3
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.3
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.3
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.2
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	1.2
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.2
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.2
LDTP01574	Importin-7 (IPO7)				C757	1.1
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.1
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.1
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.0
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP00501	Exportin-1 (XPO1)				C528	1.0
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.0
LDTP04662	Exportin-2 (CSE1L)				C842	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.6
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.2
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.2
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.2
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.0
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	0.9
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03997	Leucine-rich PPR motif-containing protein, mitochondrial (LRPPRC)				C500	20.0
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.8
LDTP10864	Calponin-2 (CNN2)				C164	1.7
LDTP14195	FH1/FH2 domain-containing protein 1 (FHOD1)				C502	1.7
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	1.7
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.7
LDTP12914	Hsp70-binding protein 1 (HSPBP1)				C204	1.7
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.7
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	1.7
LDTP05867	Treacle protein (TCOF1)				C1298	1.6
LDTP10864	Calponin-2 (CNN2)				C215	1.6
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.6
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.6
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.5
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.5
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.5
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	1.5
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.5
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.4
LDTP11890	Protein unc-45 homolog A (UNC45A)				C426	1.4
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.4
LDTP12443	Anillin (ANLN)				C712	1.4
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.4
LDTP13580	Coronin-1C (CORO1C)				C420	1.4
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.4
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.4
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.4
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.4
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.4
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.4
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.3
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.3
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.3
LDTP05867	Treacle protein (TCOF1)				C38	1.3
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.3
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.3
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.3
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.3
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	1.3
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.3
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.3
LDTP02205	Tubulin beta chain (TUBB)				C354	1.3
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.3
LDTP08238	Kinectin (KTN1)				C303	1.3
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.3
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.3
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.3
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.3
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.3
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.2
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	1.2
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	1.2
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.2
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.2
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.2
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.2
LDTP06330	Plectin (PLEC)				C3110	1.2
LDTP06330	Plectin (PLEC)				C992	1.2
LDTP04487	Cyclin-H (CCNH)				C244	1.2
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.2
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.2
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.2
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.2
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.2
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	1.2
LDTP02692	Plastin-3 (PLS3)				C33	1.2
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.2
LDTP09549	Conserved oligomeric Golgi complex subunit 1 (COG1)				C513	1.2
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.2
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	1.2
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.2
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.2
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.2
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.2
LDTP06681	Inverted formin-2 (INF2)				C332	1.1
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.1
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.1
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.1
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.1
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.1
LDTP13580	Coronin-1C (CORO1C)				C456	1.1
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.1
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.1
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.1
LDTP06330	Plectin (PLEC)				C4071	1.1
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.1
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	1.1
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.1
LDTP01532	ZW10 interactor (ZWINT)				C54	1.1
LDTP03620	Protein S100-A11 (S100A11)				C91	1.0
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.0
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.0
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.0
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C767	1.0
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.0
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	1.0
LDTP02205	Tubulin beta chain (TUBB)				C239	1.0
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.0
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	1.0
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.0
LDTP12412	Reticulon-4 (RTN4)				C1101	1.0
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	0.9
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	0.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	0.9
LDTP13925	Nucleolar protein 58 (NOP58)				C106	0.9
LDTP00768	Protein CBFA2T2 (CBFA2T2)				C111	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.8
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.8
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.8
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	0.7
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	0.7
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	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.