Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment48					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
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	3.0
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.9
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.4
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.4
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.3
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.3
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.3
LDTP02223	Cathepsin B (CTSB)				C211	1.3
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.3
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.3
LDTP02672	Elongation factor 2 (EEF2)				C41	1.3
LDTP03400	Deoxycytidine kinase (DCK)				C9	1.2
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.2
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.2
LDTP02672	Elongation factor 2 (EEF2)				C136	1.2
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.2
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.2
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	1.2
LDTP03681	DNA replication licensing factor MCM5 (MCM5)				C482	1.2
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.2
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.2
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.2
LDTP02502	Thioredoxin (TXN)				C32	1.2
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.2
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.2
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.2
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.1
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	1.1
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.1
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.1
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.1
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.1
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	1.1
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	1.1
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.1
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.1
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.1
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	1.1
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.1
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.1
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.1
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.1
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	1.1
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.1
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	1.0
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.0
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.0
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.0
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	1.0
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.0
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	1.0
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.0
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.9
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	0.9
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	0.9
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	0.8
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.7
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.5
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	1.2
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.2
LDTP00501	Exportin-1 (XPO1)				C34	1.1
LDTP04662	Exportin-2 (CSE1L)				C842	1.1
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.1
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.1
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.0

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.3
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.1
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.1

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP07037	WD repeat domain phosphoinositide-interacting protein 3 (WDR45B)				C63	1.9
LDTP12412	Reticulon-4 (RTN4)				C1101	1.8
LDTP00768	Protein CBFA2T2 (CBFA2T2)				C111	1.8
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.6
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.5
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.5
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.5
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.4
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.4
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.4
LDTP05867	Treacle protein (TCOF1)				C38	1.4
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.4
LDTP04487	Cyclin-H (CCNH)				C244	1.3
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.3
LDTP04363	Serpin H1 (SERPINH1)				C156	1.3
LDTP13580	Coronin-1C (CORO1C)				C456	1.3
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	1.3
LDTP12443	Anillin (ANLN)				C712	1.3
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.3
LDTP03620	Protein S100-A11 (S100A11)				C91	1.3
LDTP10864	Calponin-2 (CNN2)				C215	1.2
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.2
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.2
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.2
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.2
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.2
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.2
LDTP13580	Coronin-1C (CORO1C)				C420	1.2
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.2
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.2
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.2
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.2
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	1.2
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	1.1
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.1
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.1
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.1
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.1
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.1
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.1
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.1
LDTP10864	Calponin-2 (CNN2)				C164	1.1
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.1
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	1.1
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.1
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.1
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.1
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.0
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	1.0
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.0
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	1.0
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.0
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.0
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.0
LDTP04902	Actin-related protein 3 (ACTR3)				C235	1.0
LDTP08885	Actin filament-associated protein 1 (AFAP1)				C713	0.9
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	0.9
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.9
LDTP06330	Plectin (PLEC)				C992	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.