Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment32					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
LDTP03681	DNA replication licensing factor MCM5 (MCM5)				C482	20.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	20.0
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	20.0
LDTP03786	Glutaredoxin-1 (GLRX)				C23	20.0
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	20.0
LDTP13080	GMP reductase 2 (GMPR2)				C186	20.0
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	20.0
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	20.0
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	20.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	20.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	20.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	20.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	20.0
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	20.0
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	20.0
LDTP02502	Thioredoxin (TXN)				C32	20.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	20.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	20.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	19.6
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	18.2
LDTP09598	Mitochondrial coenzyme A diphosphatase NUDT8 (NUDT8)				C207	16.3
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	15.7
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	13.0
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	12.9
LDTP02672	Elongation factor 2 (EEF2)				C136	12.7
LDTP04076	Mitogen-activated protein kinase 9 (MAPK9)				C177	12.2
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	10.8
LDTP13147	Cathepsin Z (CTSZ)				C92	10.8
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	10.1
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	9.1
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	8.6
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	7.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	6.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	6.8
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	6.4
LDTP00089	Glycerol-3-phosphate phosphatase (PGP)				C297	5.7
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	5.1
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	4.4
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	4.3
LDTP07317	Tensin-3 (TNS3)				C888	4.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	3.9
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	3.8
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	3.8
LDTP13147	Cathepsin Z (CTSZ)				C173	3.8
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	3.8
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	3.7
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	3.6
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	3.6
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	3.6
LDTP05289	AMP deaminase 2 (AMPD2)				C107	3.5
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	3.5
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	3.5
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	3.3
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	3.2
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	3.1
LDTP02198	Cathepsin D (CTSD)				C117	2.9
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	2.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	2.8
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	2.7
LDTP03644	Pyrroline-5-carboxylate reductase 1, mitochondrial (PYCR1)				C120	2.6
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	2.6
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	2.5
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	2.5
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	2.4
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	2.4
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	2.3
LDTP02223	Cathepsin B (CTSB)				C211	2.3
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	2.3
LDTP03400	Deoxycytidine kinase (DCK)				C9	2.3
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	2.2
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	2.2
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	2.2
LDTP02223	Cathepsin B (CTSB)				C319	2.2
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	2.2
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	2.1
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	2.1
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	2.0
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	2.0
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.9
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	1.9
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.9
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.9
LDTP02672	Elongation factor 2 (EEF2)				C41	1.8
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	1.8
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	1.8
LDTP04424	Galactokinase (GALK1)				C182	1.8
LDTP04689	Adenosine kinase (ADK)				C353	1.7
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.7
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.7
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.7
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.7
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.7
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.7
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.7
LDTP05859	Integrin-linked protein kinase (ILK)				C346	1.6
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	1.6
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.6
LDTP03496	Protein PML (PML)				C389	1.6
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	1.5
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	1.5
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.5
LDTP01495	E3 ubiquitin-protein ligase UBR5 (UBR5)				C2267	1.5
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.4
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	1.4
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.4
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	1.3
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.3
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.3
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.3
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	1.2
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.2
LDTP04374	Dynamin-2 (DNM2)				C27	1.1
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	1.1
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.1
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.1
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.1
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	1.0
LDTP03806	ADP-ribosylation factor-like protein 3 (ARL3)				C174	1.0
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	0.9
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.8
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.8
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	20.0
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	20.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	20.0
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	17.9
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	13.0
LDTP04662	Exportin-2 (CSE1L)				C842	6.3
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	3.8
LDTP04801	Gasdermin-D (GSDMD)				C268	3.1
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	2.2
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.9
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.8
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	1.8
LDTP00501	Exportin-1 (XPO1)				C528	1.7
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	1.6
LDTP00501	Exportin-1 (XPO1)				C34	1.2
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.0
LDTP01574	Importin-7 (IPO7)				C757	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	20.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	20.0
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	15.2
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	14.6
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	9.4
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	1.8
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.2
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	1.2

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP04092	Crk-like protein (CRKL)				C249	20.0
LDTP02692	Plastin-3 (PLS3)				C33	20.0
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	20.0
LDTP13088	Protein IMPACT (IMPACT)				C195	20.0
LDTP12412	Reticulon-4 (RTN4)				C1101	20.0
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	17.1
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	15.8
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	14.3
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	13.1
LDTP05233	55 kDa erythrocyte membrane protein (MPP1)				C179	13.1
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	12.6
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	10.8
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	9.3
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	8.8
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	7.1
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	7.0
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	6.5
LDTP14195	FH1/FH2 domain-containing protein 1 (FHOD1)				C502	6.1
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	5.7
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	5.5
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	4.8
LDTP05867	Treacle protein (TCOF1)				C1298	4.8
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	4.6
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	4.5
LDTP01532	ZW10 interactor (ZWINT)				C54	4.5
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	4.4
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	4.2
LDTP11235	Protein PAXX (PAXX)				C180	4.2
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	4.2
LDTP12443	Anillin (ANLN)				C712	4.1
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	4.1
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	4.0
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	3.8
LDTP06681	Inverted formin-2 (INF2)				C332	3.7
LDTP00202	AH receptor-interacting protein (AIP)				C122	3.7
LDTP06330	Plectin (PLEC)				C992	3.5
LDTP04363	Serpin H1 (SERPINH1)				C156	3.5
LDTP04902	Actin-related protein 3 (ACTR3)				C235	3.3
LDTP12571	LanC-like protein 2 (LANCL2)				C187	3.3
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	3.3
LDTP03620	Protein S100-A11 (S100A11)				C91	3.1
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	3.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	3.1
LDTP10864	Calponin-2 (CNN2)				C164	3.0
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	2.9
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	2.9
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	2.9
LDTP05867	Treacle protein (TCOF1)				C38	2.9
LDTP02205	Tubulin beta chain (TUBB)				C354	2.6
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	2.5
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	2.5
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	2.5
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	2.5
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	2.4
LDTP10864	Calponin-2 (CNN2)				C215	2.3
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	2.3
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	2.3
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	2.3
LDTP06330	Plectin (PLEC)				C3110	2.3
LDTP13580	Coronin-1C (CORO1C)				C420	2.3
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	2.2
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	2.2
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	2.2
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	2.1
LDTP02205	Tubulin beta chain (TUBB)				C239	2.1
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	2.1
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	2.1
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	2.0
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	1.9
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	1.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	1.9
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.9
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.8
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.8
LDTP11718	Cleavage stimulation factor subunit 2 tau variant (CSTF2T)				C150	1.8
LDTP11890	Protein unc-45 homolog A (UNC45A)				C426	1.7
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.7
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	1.6
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.5
LDTP13964	MOB-like protein phocein (MOB4)				C134	1.5
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	1.5
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.5
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.5
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	1.4
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	1.3
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	1.1
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	1.1
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	1.0
LDTP13580	Coronin-1C (CORO1C)				C456	1.0
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.0
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.0
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	0.9
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	0.9
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	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.