Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment20					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
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP14036	Helicase ARIP4 (RAD54L2)				C820	20.0
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	20.0
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	20.0
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	20.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	20.0
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	20.0
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	20.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	20.0
LDTP11931	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1)				C772	20.0
LDTP13147	Cathepsin Z (CTSZ)				C92	17.5
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	17.4
LDTP02198	Cathepsin D (CTSD)				C117	12.5
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	12.2
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	12.1
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	11.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	10.6
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	8.6
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	7.1
LDTP10982	Aconitate hydratase, mitochondrial (ACO2)				C385	6.9
LDTP05859	Integrin-linked protein kinase (ILK)				C346	6.4
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	6.1
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	5.3
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	5.0
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	5.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	4.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	4.6
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	4.3
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	4.1
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	3.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	3.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	3.7
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	3.7
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	3.6
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	3.6
LDTP02223	Cathepsin B (CTSB)				C211	3.3
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	3.3
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	3.2
LDTP03496	Protein PML (PML)				C389	3.2
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	3.2
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	3.0
LDTP13147	Cathepsin Z (CTSZ)				C173	3.0
LDTP02223	Cathepsin B (CTSB)				C319	3.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	2.9
LDTP03642	Cytidine deaminase (CDA)				C14	2.8
LDTP07317	Tensin-3 (TNS3)				C888	2.8
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	2.8
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	2.6
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	2.5
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	2.5
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	2.5
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	2.4
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	2.3
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	2.1
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	2.1
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	2.1
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	2.0
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	2.0
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	2.0
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	2.0
LDTP02502	Thioredoxin (TXN)				C32	2.0
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	2.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.9
LDTP06211	Caspase-8 (CASP8)				C360	1.9
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.8
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.8
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.8
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	1.8
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.8
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.7
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.6
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.6
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.6
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.6
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.6
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.6
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.5
LDTP04689	Adenosine kinase (ADK)				C353	1.5
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.4
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	1.4
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.4
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.3
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.3
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.2
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	1.2
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.2
LDTP04374	Dynamin-2 (DNM2)				C27	1.2
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.2
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.1
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.1
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.1
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.1
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.1
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.1
LDTP02672	Elongation factor 2 (EEF2)				C41	1.1
LDTP04253	Alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1)				C522	1.0
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.0
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.0
LDTP02672	Elongation factor 2 (EEF2)				C136	1.0
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.0
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.0
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.9
LDTP01495	E3 ubiquitin-protein ligase UBR5 (UBR5)				C2267	0.9
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.8
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	0.6
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.6
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	0.5

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	20.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	17.1
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	9.4
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	2.8
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	2.0
LDTP14808	Tumor necrosis factor alpha-induced protein 2 (TNFAIP2)				C45	1.8
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.6
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.6
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.4
LDTP00501	Exportin-1 (XPO1)				C528	1.4
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.3
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.3
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.2
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.1
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.1
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	20.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	2.9
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	2.4
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	2.2
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.8
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	1.3
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.3
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.1

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP08885	Actin filament-associated protein 1 (AFAP1)				C713	20.0
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	20.0
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	20.0
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	20.0
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	20.0
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	17.2
LDTP07755	Dynamin-binding protein (DNMBP)				C691	12.0
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	9.2
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	7.0
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	6.6
LDTP18494	Tropomodulin-3 (TMOD3)				C132	6.5
LDTP06681	Inverted formin-2 (INF2)				C971	6.0
LDTP12412	Reticulon-4 (RTN4)				C1101	5.6
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	5.4
LDTP00768	Protein CBFA2T2 (CBFA2T2)				C111	5.3
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	5.2
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	5.1
LDTP06330	Plectin (PLEC)				C992	4.9
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	4.7
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	4.1
LDTP10864	Calponin-2 (CNN2)				C215	4.0
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	3.8
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	3.8
LDTP05867	Treacle protein (TCOF1)				C1298	3.7
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	3.5
LDTP06330	Plectin (PLEC)				C4071	3.4
LDTP05867	Treacle protein (TCOF1)				C38	3.4
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	3.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	3.1
LDTP10864	Calponin-2 (CNN2)				C164	3.1
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	3.1
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	3.1
LDTP13580	Coronin-1C (CORO1C)				C420	2.7
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	2.6
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	2.6
LDTP02205	Tubulin beta chain (TUBB)				C239	2.5
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	2.5
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	2.4
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	2.4
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	2.4
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	2.3
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	2.3
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	2.3
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	2.3
LDTP06681	Inverted formin-2 (INF2)				C332	2.3
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	2.3
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	2.2
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	2.2
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	2.1
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	2.1
LDTP08238	Kinectin (KTN1)				C303	2.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	2.1
LDTP11235	Protein PAXX (PAXX)				C180	2.0
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	2.0
LDTP12443	Anillin (ANLN)				C712	1.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.9
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	1.8
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.8
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.8
LDTP06330	Plectin (PLEC)				C3110	1.8
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.7
LDTP03620	Protein S100-A11 (S100A11)				C91	1.7
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.6
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.6
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	1.5
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.5
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	1.5
LDTP09549	Conserved oligomeric Golgi complex subunit 1 (COG1)				C513	1.5
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.4
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.4
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.4
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.3
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.3
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	1.3
LDTP13580	Coronin-1C (CORO1C)				C456	1.3
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.3
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.3
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.2
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.2
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.2
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.2
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	1.2
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.2
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.2
LDTP12914	Hsp70-binding protein 1 (HSPBP1)				C204	1.1
LDTP04487	Cyclin-H (CCNH)				C244	1.1
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.1
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.1
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.1
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.1
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.1
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.1
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.0
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.0
LDTP03244	Cofilin-1 (CFL1)				C80	1.0
LDTP04092	Crk-like protein (CRKL)				C249	1.0
LDTP01567	Structural maintenance of chromosomes protein 2 (SMC2)				C1174	1.0
LDTP02205	Tubulin beta chain (TUBB)				C354	1.0
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	0.9
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	0.9
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	0.8
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.8
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.7

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.