Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment27					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
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	2.9
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.8
LDTP09412	Serine/threonine-protein kinase Nek9 (NEK9)				C623	1.5
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.5
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.5
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.4
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.3
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	1.3
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.2
LDTP15484	Saccharopine dehydrogenase-like oxidoreductase (SCCPDH)				C238	1.2
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.2
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	1.2
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	1.2
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.2
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.2
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	1.1
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	1.1
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.1
LDTP04424	Galactokinase (GALK1)				C182	1.1
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.1
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	1.1
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	1.1
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	1.1
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	1.1
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	1.1
LDTP11107	Serine/threonine-protein phosphatase CPPED1 (CPPED1)				C54	1.1
LDTP11340	Cyclin-dependent kinase 19 (CDK19)				C349	1.1
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.1
LDTP09912	DNA repair protein RAD50 (RAD50)				C102	1.1
LDTP03496	Protein PML (PML)				C389	1.1
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.1
LDTP03642	Cytidine deaminase (CDA)				C14	1.1
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.1
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.1
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	1.1
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.1
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.1
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.1
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.1
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.1
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	1.0
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	1.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.0
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.0
LDTP07098	Probable ATP-dependent RNA helicase DDX59 (DDX59)				C453	1.0
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.0
LDTP02198	Cathepsin D (CTSD)				C117	1.0
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.0
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.0
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	1.0
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.0
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.0
LDTP01470	Lysine-specific demethylase 4B (KDM4B)				C694	1.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.0
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	1.0
LDTP07110	Putative transferase CAF17, mitochondrial (IBA57)				C170	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	1.0
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.0
LDTP11931	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1)				C772	1.0
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.0
LDTP02223	Cathepsin B (CTSB)				C319	1.0
LDTP13080	GMP reductase 2 (GMPR2)				C186	1.0
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	0.9
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.9
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	0.9
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	0.9
LDTP02672	Elongation factor 2 (EEF2)				C41	0.9
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	0.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	0.9
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	0.9
LDTP02502	Thioredoxin (TXN)				C32	0.9
LDTP11030	Serine/threonine-protein kinase VRK1 (VRK1)				C50	0.9
LDTP02672	Elongation factor 2 (EEF2)				C136	0.9
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	0.9
LDTP04374	Dynamin-2 (DNM2)				C27	0.9
LDTP14036	Helicase ARIP4 (RAD54L2)				C820	0.9
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	0.9
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	0.9
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.9
LDTP10002	Ribonuclease P/MRP protein subunit POP5 (POP5)				C146	0.9
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	0.9
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	0.9
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.9
LDTP04689	Adenosine kinase (ADK)				C353	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.8
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.8
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	1.3
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	1.1
LDTP04662	Exportin-2 (CSE1L)				C842	1.1
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.0
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.0
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.0
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.0
LDTP00501	Exportin-1 (XPO1)				C34	1.0
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.9
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	0.9
LDTP00501	Exportin-1 (XPO1)				C528	0.9
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	0.8
LDTP14808	Tumor necrosis factor alpha-induced protein 2 (TNFAIP2)				C45	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.2
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.1
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.0
LDTP02016	Glucocorticoid receptor (NR3C1)				C302	1.0
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	1.0
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.0
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	1.0
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	1.0
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	0.9

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP03244	Cofilin-1 (CFL1)				C80	20.0
LDTP13925	Nucleolar protein 58 (NOP58)				C106	1.7
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.6
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	1.3
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.2
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.2
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.2
LDTP05867	Treacle protein (TCOF1)				C38	1.2
LDTP10864	Calponin-2 (CNN2)				C164	1.2
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	1.2
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.2
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.2
LDTP08573	Ankyrin repeat and KH domain-containing protein 1 (ANKHD1)				C615	1.1
LDTP06330	Plectin (PLEC)				C992	1.1
LDTP06330	Plectin (PLEC)				C4071	1.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.1
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.1
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.1
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	1.1
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.1
LDTP04078	Proliferation marker protein Ki-67 (MKI67)				C903	1.1
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	1.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.1
LDTP05867	Treacle protein (TCOF1)				C1298	1.1
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.1
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.1
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.1
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.1
LDTP08238	Kinectin (KTN1)				C303	1.1
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	1.1
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.1
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	1.1
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.1
LDTP03620	Protein S100-A11 (S100A11)				C91	1.0
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.0
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	1.0
LDTP13580	Coronin-1C (CORO1C)				C420	1.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.0
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	1.0
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.0
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.0
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.0
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.0
LDTP02205	Tubulin beta chain (TUBB)				C239	1.0
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.0
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.0
LDTP02205	Tubulin beta chain (TUBB)				C354	1.0
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	1.0
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	1.0
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.0
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	1.0
LDTP06330	Plectin (PLEC)				C3110	1.0
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.0
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.0
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.0
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	1.0
LDTP04487	Cyclin-H (CCNH)				C244	1.0
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.0
LDTP01532	ZW10 interactor (ZWINT)				C54	1.0
LDTP12443	Anillin (ANLN)				C712	0.9
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	0.9
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	0.9
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	0.9
LDTP00727	U4/U6.U5 tri-snRNP-associated protein 1 (SART1)				C645	0.9
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	0.9
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	0.9
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	0.9
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	0.9
LDTP04092	Crk-like protein (CRKL)				C249	0.9
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	0.9
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	0.9
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	0.9
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	0.9
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	0.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	0.9
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	0.9
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	0.9
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.8
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	0.8
LDTP00768	Protein CBFA2T2 (CBFA2T2)				C111	0.8
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	0.8
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.8
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	0.8
LDTP04518	DNA mismatch repair protein Msh6 (MSH6)				C1117	0.7
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	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.