Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment6					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
LDTP02733	Pyruvate kinase PKM (PKM)				C423	20.0
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	1.9
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.8
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.8
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.7
LDTP13147	Cathepsin Z (CTSZ)				C92	1.7
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.7
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.6
LDTP04374	Dynamin-2 (DNM2)				C27	1.6
LDTP05992	Bleomycin hydrolase (BLMH)				C73	1.6
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.5
LDTP02502	Thioredoxin (TXN)				C32	1.5
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.5
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	1.5
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.4
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.4
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.4
LDTP02198	Cathepsin D (CTSD)				C117	1.4
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.3
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.3
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.3
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.3
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.3
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.3
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.3
LDTP02672	Elongation factor 2 (EEF2)				C41	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.2
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.2
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.2
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.2
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.2
LDTP10774	Elongation factor G, mitochondrial (GFM1)				C153	1.2
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.2
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.2
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.2
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.2
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.2
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.2
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.2
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.2
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.1
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	1.1
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	1.1
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.1
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.1
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.1
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	1.1
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.1
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.1
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.1
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.1
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.1
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.1
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.1
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.0
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	1.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.0
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.0
LDTP00701	D-3-phosphoglycerate dehydrogenase (PHGDH)				C369	1.0
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.0
LDTP12190	NmrA-like family domain-containing protein 1 (NMRAL1)				C154	1.0
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	1.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	1.0
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.0
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	0.9
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	0.9
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	0.9
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.8
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	0.8
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	0.8
LDTP03642	Cytidine deaminase (CDA)				C14	0.7
LDTP02672	Elongation factor 2 (EEF2)				C136	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP04662	Exportin-2 (CSE1L)				C842	1.8
LDTP04801	Gasdermin-D (GSDMD)				C268	1.7
LDTP01574	Importin-7 (IPO7)				C757	1.6
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.5
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.4
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.3
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.2
LDTP00501	Exportin-1 (XPO1)				C34	1.2
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.2
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.1
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	1.0
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	1.0
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.9
LDTP00501	Exportin-1 (XPO1)				C528	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.7
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.6
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.5
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	1.1
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.1
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	20.0
LDTP04902	Actin-related protein 3 (ACTR3)				C235	2.9
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	2.9
LDTP03244	Cofilin-1 (CFL1)				C80	2.5
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	2.2
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.9
LDTP06330	Plectin (PLEC)				C4071	1.8
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.8
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	1.8
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.7
LDTP06330	Plectin (PLEC)				C992	1.6
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.5
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.4
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.4
LDTP04487	Cyclin-H (CCNH)				C244	1.3
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.3
LDTP11235	Protein PAXX (PAXX)				C180	1.3
LDTP06681	Inverted formin-2 (INF2)				C971	1.3
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.3
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	1.3
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.3
LDTP06681	Inverted formin-2 (INF2)				C332	1.3
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.3
LDTP05867	Treacle protein (TCOF1)				C38	1.3
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.3
LDTP02692	Plastin-3 (PLS3)				C33	1.3
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	1.3
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.3
LDTP08238	Kinectin (KTN1)				C303	1.2
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.2
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.2
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.2
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.2
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.2
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.2
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.2
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.2
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.2
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.2
LDTP03620	Protein S100-A11 (S100A11)				C91	1.2
LDTP10864	Calponin-2 (CNN2)				C164	1.1
LDTP07755	Dynamin-binding protein (DNMBP)				C691	1.1
LDTP13580	Coronin-1C (CORO1C)				C420	1.1
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.1
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	1.1
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.1
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.1
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.1
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.1
LDTP06330	Plectin (PLEC)				C3110	1.1
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.1
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.0
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	1.0
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	1.0
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.0
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.0
LDTP05867	Treacle protein (TCOF1)				C1298	1.0
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.0
LDTP13925	Nucleolar protein 58 (NOP58)				C106	1.0
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.0
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.0
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	0.9
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	0.9
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	0.9
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	0.9
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	0.9
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	0.8

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.