Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment46					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
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	1.5
LDTP07110	Putative transferase CAF17, mitochondrial (IBA57)				C170	1.5
LDTP02223	Cathepsin B (CTSB)				C211	1.4
LDTP04424	Galactokinase (GALK1)				C182	1.3
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	1.3
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	1.2
LDTP02198	Cathepsin D (CTSD)				C117	1.2
LDTP08135	E3 ubiquitin-protein ligase HUWE1 (HUWE1)				C4367	1.2
LDTP13147	Cathepsin Z (CTSZ)				C173	1.2
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.2
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.1
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	1.1
LDTP03496	Protein PML (PML)				C389	1.1
LDTP10002	Ribonuclease P/MRP protein subunit POP5 (POP5)				C146	1.1
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	1.1
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.1
LDTP03400	Deoxycytidine kinase (DCK)				C45	1.1
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	1.1
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	1.1
LDTP03642	Cytidine deaminase (CDA)				C14	1.1
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	1.1
LDTP03163	Sterol carrier protein 2 (SCP2)				C94	1.1
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	1.1
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.0
LDTP04374	Dynamin-2 (DNM2)				C27	1.0
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.0
LDTP05992	Bleomycin hydrolase (BLMH)				C73	1.0
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.0
LDTP09446	Ribonuclease H2 subunit C (RNASEH2C)				C34	1.0
LDTP11111	Tudor-interacting repair regulator protein (NUDT16L1)				C88	1.0
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	1.0
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.0
LDTP02502	Thioredoxin (TXN)				C32	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.0
LDTP07317	Tensin-3 (TNS3)				C888	1.0
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	1.0
LDTP01245	Enoyl-CoA delta isomerase 2 (ECI2)				C380	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	1.0
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.0
LDTP02223	Cathepsin B (CTSB)				C319	1.0
LDTP15311	Deaminated glutathione amidase (NIT1)				C203	1.0
LDTP15306	Transmembrane protease serine 12 (TMPRSS12)				C64	1.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	1.0
LDTP14159	Ubiquitin carboxyl-terminal hydrolase 16 (USP16)				C205	1.0
LDTP02672	Elongation factor 2 (EEF2)				C41	1.0
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	1.0
LDTP16095	Ethylmalonyl-CoA decarboxylase (ECHDC1)				C133	1.0
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	1.0
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	1.0
LDTP06643	Uridine phosphorylase 1 (UPP1)				C162	1.0
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.0
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.0
LDTP02693	Acylamino-acid-releasing enzyme (APEH)				C641	1.0
LDTP09338	NEDD8-activating enzyme E1 catalytic subunit (UBA3)				C237	1.0
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	1.0
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	0.9
LDTP02672	Elongation factor 2 (EEF2)				C136	0.9
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	0.9
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	0.9
LDTP00482	Peripheral plasma membrane protein CASK (CASK)				C914	0.9
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	0.9
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.9
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	0.9
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	0.9
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	0.9
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	0.9
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	0.9
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C918	0.9
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	0.9
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	0.9
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	0.9
LDTP04690	Double-stranded RNA-specific adenosine deaminase (ADAR)				C1224	0.9
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	0.9
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	0.9
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	0.9
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	0.9
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	0.9
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	0.9
LDTP13080	GMP reductase 2 (GMPR2)				C186	0.9
LDTP09598	Mitochondrial coenzyme A diphosphatase NUDT8 (NUDT8)				C207	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	0.9
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	0.9
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	0.9
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	0.9
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.9
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	0.9
LDTP10801	ATPase WRNIP1 (WRNIP1)				C272	0.9
LDTP05859	Integrin-linked protein kinase (ILK)				C346	0.9
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	0.8
LDTP04251	Elongation factor Tu, mitochondrial (TUFM)				C147	0.8
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	0.8
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	0.8
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	0.8
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	0.8
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	0.8
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	0.8
LDTP04689	Adenosine kinase (ADK)				C353	0.8
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.8
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	0.8
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	0.8
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	0.8
LDTP04306	Adenosine 5'-monophosphoramidase HINT1 (HINT1)				C84	0.8
LDTP13147	Cathepsin Z (CTSZ)				C92	0.8
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	0.8
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	0.8
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	0.8
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	0.8
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	0.8
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	0.8
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	0.8
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	0.8
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	0.7
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.7
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	0.7
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.7
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.6
LDTP03806	ADP-ribosylation factor-like protein 3 (ARL3)				C174	0.6
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	0.6
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.6
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	0.6
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	0.6
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C100	0.4
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	0.2

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.2
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	1.1
LDTP08769	Nuclear pore complex protein Nup93 (NUP93)				C522	1.1
LDTP00501	Exportin-1 (XPO1)				C34	1.0
LDTP04662	Exportin-2 (CSE1L)				C842	1.0
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.0
LDTP09204	Nucleoporin NUP35 (NUP35)				C255	0.9
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	0.9
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.9
LDTP04707	Protein SEC13 homolog (SEC13)				C187	0.9
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	0.9
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	0.9
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	0.8
LDTP08315	THO complex subunit 6 homolog (THOC6)				C35	0.8
LDTP04801	Gasdermin-D (GSDMD)				C268	0.8
LDTP03327	ATP synthase subunit alpha, mitochondrial (ATP5F1A)				C294	0.8
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	0.8
LDTP00501	Exportin-1 (XPO1)				C528	0.7

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	1.9
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	1.2
LDTP12507	Chromatin accessibility complex protein 1 (CHRAC1)				C55	1.2
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	1.0
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	1.0
LDTP05485	Recombining binding protein suppressor of hairless (RBPJ)				C313	0.9
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	0.9
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	0.9
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	2.0
LDTP06330	Plectin (PLEC)				C992	1.6
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	1.5
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	1.4
LDTP12412	Reticulon-4 (RTN4)				C1101	1.4
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	1.3
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	1.3
LDTP06250	Proteasome activator complex subunit 4 (PSME4)				C1840	1.3
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.2
LDTP11235	Protein PAXX (PAXX)				C180	1.2
LDTP18494	Tropomodulin-3 (TMOD3)				C132	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	1.2
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.2
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.2
LDTP10843	MMS19 nucleotide excision repair protein homolog (MMS19)				C848	1.2
LDTP00430	Transcription elongation regulator 1 (TCERG1)				C1062	1.2
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.1
LDTP03620	Protein S100-A11 (S100A11)				C91	1.1
LDTP05867	Treacle protein (TCOF1)				C38	1.1
LDTP05233	55 kDa erythrocyte membrane protein (MPP1)				C179	1.1
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.1
LDTP02205	Tubulin beta chain (TUBB)				C239	1.1
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.1
LDTP10864	Calponin-2 (CNN2)				C215	1.1
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	1.1
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.1
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	1.1
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.1
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	1.1
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	1.1
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	1.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.0
LDTP04363	Serpin H1 (SERPINH1)				C156	1.0
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	1.0
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	1.0
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.0
LDTP12443	Anillin (ANLN)				C712	1.0
LDTP13580	Coronin-1C (CORO1C)				C420	1.0
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	1.0
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.0
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.0
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	1.0
LDTP10864	Calponin-2 (CNN2)				C164	1.0
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	1.0
LDTP10284	Multivesicular body subunit 12A (MVB12A)				C231	1.0
LDTP12638	Protein lin-7 homolog C (LIN7C)				C47	1.0
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	1.0
LDTP02692	Plastin-3 (PLS3)				C33	1.0
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.0
LDTP12144	GrpE protein homolog 1, mitochondrial (GRPEL1)				C124	1.0
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	1.0
LDTP08573	Ankyrin repeat and KH domain-containing protein 1 (ANKHD1)				C615	1.0
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	1.0
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	1.0
LDTP02205	Tubulin beta chain (TUBB)				C354	1.0
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.0
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	1.0
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	0.9
LDTP05867	Treacle protein (TCOF1)				C1298	0.9
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	0.9
LDTP06681	Inverted formin-2 (INF2)				C332	0.9
LDTP06330	Plectin (PLEC)				C3110	0.9
LDTP13580	Coronin-1C (CORO1C)				C456	0.9
LDTP13925	Nucleolar protein 58 (NOP58)				C106	0.9
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	0.9
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	0.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	0.9
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	0.9
LDTP04902	Actin-related protein 3 (ACTR3)				C235	0.9
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	0.9
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	0.9
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	0.9
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	0.9
LDTP04487	Cyclin-H (CCNH)				C244	0.9
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.9
LDTP14351	RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMOC1)				C179	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.8
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	0.8
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	0.8
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	0.8
LDTP03865	Large ribosomal subunit protein uL3 (RPL3)				C253	0.8
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	0.8
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.8
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	0.8
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	0.8
LDTP04517	Transcription initiation factor IIA subunit 2 (GTF2A2)				C68	0.8
LDTP06681	Inverted formin-2 (INF2)				C971	0.8
LDTP13964	MOB-like protein phocein (MOB4)				C134	0.8
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	0.8
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	0.8
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	0.8
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	0.8
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	0.8
LDTP04092	Crk-like protein (CRKL)				C249	0.8
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.7
LDTP13837	Trafficking protein particle complex subunit 4 (TRAPPC4)				C195	0.7
LDTP15730	Ataxin-7-like protein 3B (ATXN7L3B)				C75	0.5

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.