Probe Name	IA-alkyne					Probe Info
Probe concentration	100 uM
Criteria	Quantification: Probe vs (Probe+Competitor)
Quantitative Method	Isotope tag
Competitor Name	Fragment25					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
LDTP04211	Isocitrate dehydrogenase [NADP], mitochondrial (IDH2)				C308	14.5
LDTP05128	Glutathione S-transferase omega-1 (GSTO1)				C32	2.8
LDTP02333	Glutathione S-transferase P (GSTP1)				C48	1.8
LDTP12627	Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2)				C22	1.7
LDTP05070	Ubiquitin-conjugating enzyme E2 L3 (UBE2L3)				C86	1.5
LDTP01633	Persulfide dioxygenase ETHE1, mitochondrial (ETHE1)				C170	1.4
LDTP00601	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT)				C620	1.4
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C179	1.3
LDTP02765	Aldo-keto reductase family 1 member B1 (AKR1B1)				C299	1.3
LDTP04374	Dynamin-2 (DNM2)				C27	1.3
LDTP14888	Pre-rRNA-processing protein TSR1 homolog (TSR1)				C126	1.3
LDTP10418	Mannose-1-phosphate guanyltransferase alpha (GMPPA)				C389	1.2
LDTP10386	ERO1-like protein alpha (ERO1A)				C37	1.1
LDTP12960	[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial (PDP1)				C149	1.1
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C193	1.1
LDTP05373	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1)				C680	1.1
LDTP03223	Small ribosomal subunit protein uS3 (RPS3)				C97	1.1
LDTP10929	Cell cycle checkpoint control protein RAD9A (RAD9A)				C114	1.1
LDTP02329	3-ketoacyl-CoA thiolase, peroxisomal (ACAA1)				C381	1.1
LDTP13449	Cleavage and polyadenylation specificity factor subunit 3 (CPSF3)				C498	1.1
LDTP03642	Cytidine deaminase (CDA)				C14	1.1
LDTP12428	Omega-amidase NIT2 (NIT2)				C153	1.1
LDTP04689	Adenosine kinase (ADK)				C353	1.0
LDTP17082	Isoamyl acetate-hydrolyzing esterase 1 homolog (IAH1)				C137	1.0
LDTP03998	3-ketoacyl-CoA thiolase, mitochondrial (ACAA2)				C92	1.0
LDTP02911	Calpain-2 catalytic subunit (CAPN2)				C640	1.0
LDTP13147	Cathepsin Z (CTSZ)				C92	1.0
LDTP13663	Dual specificity protein phosphatase 12 (DUSP12)				C265	1.0
LDTP08181	Glutaredoxin-related protein 5, mitochondrial (GLRX5)				C67	1.0
LDTP07651	Monofunctional C1-tetrahydrofolate synthase, mitochondrial (MTHFD1L)				C906	1.0
LDTP05912	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)				C113	1.0
LDTP06314	Protein disulfide-isomerase A6 (PDIA6)				C55	1.0
LDTP06621	Ubiquitin-conjugating enzyme E2 S (UBE2S)				C118	1.0
LDTP06211	Caspase-8 (CASP8)				C360	1.0
LDTP09912	DNA repair protein RAD50 (RAD50)				C102	1.0
LDTP10386	ERO1-like protein alpha (ERO1A)				C241	1.0
LDTP02552	Glycogen phosphorylase, brain form (PYGB)				C326	1.0
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C140	1.0
LDTP01333	Isocitrate dehydrogenase [NADP] cytoplasmic (IDH1)				C269	1.0
LDTP10997	Protein arginine N-methyltransferase 1 (PRMT1)				C109	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C206	1.0
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C377	1.0
LDTP14155	Serine/threonine-protein kinase MRCK beta (CDC42BPB)				C1517	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C119	1.0
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C413	1.0
LDTP10982	Aconitate hydratase, mitochondrial (ACO2)				C385	1.0
LDTP02198	Cathepsin D (CTSD)				C117	1.0
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C217	1.0
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C347	1.0
LDTP02038	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)				C152	1.0
LDTP03521	Protein disulfide-isomerase A3 (PDIA3)				C406	1.0
LDTP02677	Protein disulfide-isomerase A4 (PDIA4)				C555	1.0
LDTP02733	Pyruvate kinase PKM (PKM)				C423	1.0
LDTP14535	6-phosphogluconolactonase (PGLS)				C32	1.0
LDTP02522	60 kDa heat shock protein, mitochondrial (HSPD1)				C442	1.0
LDTP02502	Thioredoxin (TXN)				C32	1.0
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C129	1.0
LDTP03159	Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS)				C374	0.9
LDTP09912	DNA repair protein RAD50 (RAD50)				C1302	0.9
LDTP03000	General transcription and DNA repair factor IIH helicase subunit XPB (ERCC3)				C342	0.9
LDTP16025	Ketosamine-3-kinase (FN3KRP)				C24	0.9
LDTP10878	Parkinson disease protein 7 (PARK7)				C106	0.9
LDTP06338	Prostaglandin E synthase 3 (PTGES3)				C58	0.9
LDTP03152	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT1)				C102	0.9
LDTP17247	5'-nucleotidase domain-containing protein 1 (NT5DC1)				C119	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C196	0.9
LDTP05289	AMP deaminase 2 (AMPD2)				C107	0.9
LDTP04103	Dual specificity mitogen-activated protein kinase kinase 3 (MAP2K3)				C207	0.9
LDTP09067	Thioredoxin domain-containing protein 5 (TXNDC5)				C350	0.9
LDTP10954	3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10)				C214	0.9
LDTP03291	Acetyl-CoA acetyltransferase, mitochondrial (ACAT1)				C126	0.9
LDTP06150	DNA replication licensing factor MCM6 (MCM6)				C301	0.9
LDTP02672	Elongation factor 2 (EEF2)				C41	0.9
LDTP02611	Inosine-5'-monophosphate dehydrogenase 2 (IMPDH2)				C331	0.9
LDTP03512	Peroxiredoxin-5, mitochondrial (PRDX5)				C204	0.9
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C315	0.9
LDTP02223	Cathepsin B (CTSB)				C319	0.9
LDTP02672	Elongation factor 2 (EEF2)				C136	0.9
LDTP02022	Thymidine kinase, cytosolic (TK1)				C66	0.9
LDTP02223	Cathepsin B (CTSB)				C211	0.9
LDTP09912	DNA repair protein RAD50 (RAD50)				C1296	0.9
LDTP03786	Glutaredoxin-1 (GLRX)				C23	0.9
LDTP12166	Ras-related GTP-binding protein C (RRAGC)				C358	0.9
LDTP07098	Probable ATP-dependent RNA helicase DDX59 (DDX59)				C453	0.9
LDTP00273	Dynamin-1-like protein (DNM1L)				C367	0.9
LDTP05859	Integrin-linked protein kinase (ILK)				C346	0.9
LDTP05773	Peroxiredoxin-4 (PRDX4)				C51	0.9
LDTP02188	Protein disulfide-isomerase (P4HB)				C397	0.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C347	0.9
LDTP03496	Protein PML (PML)				C389	0.9
LDTP04601	Arginine--tRNA ligase, cytoplasmic (RARS1)				C34	0.9
LDTP03146	Protein-glutamine gamma-glutamyltransferase 2 (TGM2)				C277	0.9
LDTP04265	Serine--tRNA ligase, cytoplasmic (SARS1)				C438	0.9
LDTP07907	Tubulin alpha-1A chain (TUBA1A)				C376	0.9
LDTP02022	Thymidine kinase, cytosolic (TK1)				C230	0.9
LDTP10386	ERO1-like protein alpha (ERO1A)				C166	0.8
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C322	0.8
LDTP05075	Tubulin alpha-4A chain (TUBA4A)				C295	0.8
LDTP00246	Eukaryotic translation initiation factor 3 subunit F (EIF3F)				C256	0.8
LDTP10177	Medium-chain acyl-CoA ligase ACSF2, mitochondrial (ACSF2)				C64	0.8
LDTP02580	C-1-tetrahydrofolate synthase, cytoplasmic (MTHFD1)				C863	0.8
LDTP02576	Pyruvate carboxylase, mitochondrial (PC)				C622	0.8
LDTP03400	Deoxycytidine kinase (DCK)				C9	0.8
LDTP03400	Deoxycytidine kinase (DCK)				C45	0.8
LDTP11388	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NAA15)				C721	0.8
LDTP12837	Mitogen-activated protein kinase kinase kinase 20 (MAP3K20)				C22	0.8
LDTP01005	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 (PLOD3)				C691	0.7
LDTP05314	ATP-dependent 6-phosphofructokinase, platelet type (PFKP)				C641	0.7
LDTP06199	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D)				C17	0.7
LDTP04987	26S proteasome regulatory subunit 10B (PSMC6)				C170	0.6
LDTP04061	26S proteasome regulatory subunit 6B (PSMC4)				C210	0.6
LDTP04077	Dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4)				C246	0.5
LDTP03299	Cyclin-dependent kinase 2 (CDK2)				C177	0.5

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP11873	Thioredoxin-interacting protein (TXNIP)				C170	1.2
LDTP05057	Small ribosomal subunit protein RACK1 (RACK1)				C182	1.2
LDTP13490	Apoptotic chromatin condensation inducer in the nucleus (ACIN1)				C1223	1.1
LDTP04801	Gasdermin-D (GSDMD)				C268	1.1
LDTP04259	Signal recognition particle 9 kDa protein (SRP9)				C48	1.1
LDTP00196	Unconventional myosin-Ic (MYO1C)				C802	1.1
LDTP04707	Protein SEC13 homolog (SEC13)				C187	1.0
LDTP13661	Sorting nexin-6 (SNX6)				C264	1.0
LDTP11103	Thioredoxin domain-containing protein 17 (TXNDC17)				C43	1.0
LDTP00244	Chloride intracellular channel protein 1 (CLIC1)				C24	1.0
LDTP04662	Exportin-2 (CSE1L)				C842	0.9
LDTP00501	Exportin-1 (XPO1)				C34	0.9
LDTP03777	Nuclear pore complex protein Nup214 (NUP214)				C728	0.9
LDTP14222	Chloride intracellular channel protein 4 (CLIC4)				C35	0.8

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP01191	Zinc finger protein 217 (ZNF217)				C286	20.0
LDTP09311	SWI/SNF complex subunit SMARCC2 (SMARCC2)				C145	0.9
LDTP06341	Non-POU domain-containing octamer-binding protein (NONO)				C145	0.9
LDTP12792	CDKN2A-interacting protein (CDKN2AIP)				C516	0.9
LDTP10756	Nucleus accumbens-associated protein 1 (NACC1)				C416	0.9
LDTP03969	Signal transducer and activator of transcription 1-alpha/beta (STAT1)				C492	0.8
LDTP07940	eIF5-mimic protein 2 (BZW1)				C35	0.6

Target ID	Target Name				Binding Sites	Binding Ratio
LDTP10299	Enhancer of mRNA-decapping protein 3 (EDC3)				C413	20.0
LDTP04110	Small ribosomal subunit protein uS7 (RPS5)				C66	1.6
LDTP12737	BRISC and BRCA1-A complex member 1 (BABAM1)				C222	1.4
LDTP11239	Protein misato homolog 1 (MSTO1)				C403	1.4
LDTP06684	Sister chromatid cohesion protein PDS5 homolog A (PDS5A)				C242	1.4
LDTP05259	Heterogeneous nuclear ribonucleoprotein U (HNRNPU)				C562	1.4
LDTP06330	Plectin (PLEC)				C4071	1.3
LDTP15677	Ribosomal protein eL42-like (RPL36AL)				C88	1.3
LDTP13583	Targeting protein for Xklp2 (TPX2)				C536	1.2
LDTP13591	A-kinase anchor protein 8-like (AKAP8L)				C211	1.2
LDTP01320	Eukaryotic translation initiation factor 3 subunit J (EIF3J)				C207	1.2
LDTP11191	WW domain-containing adapter protein with coiled-coil (WAC)				C553	1.2
LDTP03665	Cleavage stimulation factor subunit 2 (CSTF2)				C150	1.1
LDTP03695	Heat shock 70 kDa protein 4 (HSPA4)				C34	1.1
LDTP04117	Ras GTPase-activating-like protein IQGAP1 (IQGAP1)				C781	1.1
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C267	1.1
LDTP03841	Hippocalcin-like protein 1 (HPCAL1)				C185	1.1
LDTP06378	Disks large-associated protein 5 (DLGAP5)				C129	1.1
LDTP01532	ZW10 interactor (ZWINT)				C54	1.1
LDTP05233	55 kDa erythrocyte membrane protein (MPP1)				C179	1.1
LDTP02692	Plastin-3 (PLS3)				C33	1.1
LDTP06681	Inverted formin-2 (INF2)				C971	1.1
LDTP11239	Protein misato homolog 1 (MSTO1)				C485	1.1
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C36	1.1
LDTP10990	T-complex protein 1 subunit eta (CCT7)				C29	1.0
LDTP12571	LanC-like protein 2 (LANCL2)				C187	1.0
LDTP05867	Treacle protein (TCOF1)				C1298	1.0
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C291	1.0
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C618	1.0
LDTP05597	Neuroblast differentiation-associated protein AHNAK (AHNAK)				C108	1.0
LDTP02205	Tubulin beta chain (TUBB)				C239	1.0
LDTP06082	Dynactin subunit 1 (DCTN1)				C1252	1.0
LDTP11197	Mini-chromosome maintenance complex-binding protein (MCMBP)				C325	1.0
LDTP04971	Small ribosomal subunit protein uS12 (RPS23)				C90	1.0
LDTP06281	Condensin complex subunit 1 (NCAPD2)				C767	1.0
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C561	1.0
LDTP05484	Proteasome activator complex subunit 1 (PSME1)				C22	1.0
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C60	1.0
LDTP03987	Small ribosomal subunit protein eS27 (RPS27)				C77	1.0
LDTP05770	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2)				C23	1.0
LDTP13817	Nuclear migration protein nudC (NUDC)				C188	0.9
LDTP03620	Protein S100-A11 (S100A11)				C91	0.9
LDTP04201	T-complex protein 1 subunit epsilon (CCT5)				C253	0.9
LDTP11890	Protein unc-45 homolog A (UNC45A)				C426	0.9
LDTP05930	SNW domain-containing protein 1 (SNW1)				C250	0.9
LDTP02631	Alpha-actinin-1 (ACTN1)				C370	0.9
LDTP03395	Large ribosomal subunit protein uL16 (RPL10)				C105	0.9
LDTP13964	MOB-like protein phocein (MOB4)				C134	0.9
LDTP18494	Tropomodulin-3 (TMOD3)				C132	0.9
LDTP11212	Tubulin-specific chaperone D (TBCD)				C850	0.9
LDTP00552	Actin-related protein 2/3 complex subunit 3 (ARPC3)				C162	0.9
LDTP11235	Protein PAXX (PAXX)				C180	0.9
LDTP12443	Anillin (ANLN)				C712	0.9
LDTP04560	Cytosolic Fe-S cluster assembly factor NUBP1 (NUBP1)				C235	0.9
LDTP06244	Nuclear mitotic apparatus protein 1 (NUMA1)				C961	0.9
LDTP01011	Protein diaphanous homolog 1 (DIAPH1)				C1227	0.9
LDTP06330	Plectin (PLEC)				C3110	0.9
LDTP13580	Coronin-1C (CORO1C)				C456	0.9
LDTP06362	Leucine-rich repeat-containing protein 41 (LRRC41)				C297	0.9
LDTP04975	Small ribosomal subunit protein uS17 (RPS11)				C116	0.9
LDTP03244	Cofilin-1 (CFL1)				C80	0.9
LDTP13580	Coronin-1C (CORO1C)				C420	0.9
LDTP15701	EF-hand domain-containing protein D2 (EFHD2)				C172	0.9
LDTP07088	Formin-binding protein 1-like (FNBP1L)				C69	0.9
LDTP00756	Heterogeneous nuclear ribonucleoprotein R (HNRNPR)				C99	0.9
LDTP05186	Large ribosomal subunit protein eL24 (RPL24)				C6	0.9
LDTP05008	Large ribosomal subunit protein uL14 (RPL23)				C28	0.9
LDTP10771	Mediator of RNA polymerase II transcription subunit 15 (MED15)				C660	0.9
LDTP13088	Protein IMPACT (IMPACT)				C195	0.9
LDTP06268	Condensin complex subunit 2 (NCAPH)				C418	0.9
LDTP12754	H/ACA ribonucleoprotein complex subunit 2 (NHP2)				C18	0.9
LDTP12685	Integrator complex subunit 13 (INTS13)				C349	0.9
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C280	0.9
LDTP08573	Ankyrin repeat and KH domain-containing protein 1 (ANKHD1)				C615	0.9
LDTP10864	Calponin-2 (CNN2)				C164	0.9
LDTP06681	Inverted formin-2 (INF2)				C332	0.9
LDTP10864	Calponin-2 (CNN2)				C215	0.8
LDTP10613	Dedicator of cytokinesis protein 7 (DOCK7)				C2125	0.8
LDTP06083	Cytoplasmic dynein 1 heavy chain 1 (DYNC1H1)				C1999	0.8
LDTP10781	NudC domain-containing protein 1 (NUDCD1)				C376	0.8
LDTP09580	Programmed cell death 6-interacting protein (PDCD6IP)				C250	0.8
LDTP04363	Serpin H1 (SERPINH1)				C156	0.8
LDTP02511	cAMP-dependent protein kinase type I-alpha regulatory subunit (PRKAR1A)				C18	0.8
LDTP03860	Stress-70 protein, mitochondrial (HSPA9)				C317	0.8
LDTP04487	Cyclin-H (CCNH)				C244	0.8
LDTP13979	Cytosolic iron-sulfur assembly component 2B (CIAO2B)				C93	0.8
LDTP00463	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)				C343	0.8
LDTP03815	Large ribosomal subunit protein uL4 (RPL4)				C96	0.8
LDTP12669	Mediator of RNA polymerase II transcription subunit 17 (MED17)				C649	0.8
LDTP04997	Small ribosomal subunit protein eS4, X isoform (RPS4X)				C41	0.8
LDTP02934	T-complex protein 1 subunit alpha (TCP1)				C76	0.8
LDTP12651	TBC1 domain family member 23 (TBC1D23)				C283	0.8
LDTP05867	Treacle protein (TCOF1)				C38	0.8
LDTP04092	Crk-like protein (CRKL)				C249	0.8
LDTP07947	Eukaryotic translation initiation factor 3 subunit M (EIF3M)				C134	0.8
LDTP04514	Heterogeneous nuclear ribonucleoprotein F (HNRNPF)				C122	0.8
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C341	0.8
LDTP12780	THUMP domain-containing protein 1 (THUMPD1)				C31	0.8
LDTP03967	Lamina-associated polypeptide 2, isoform alpha (TMPO)				C684	0.8
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C109	0.8
LDTP01567	Structural maintenance of chromosomes protein 2 (SMC2)				C1174	0.8
LDTP06542	Cysteine and glycine-rich protein 2 (CSRP2)				C33	0.8
LDTP04390	T-complex protein 1 subunit theta (CCT8)				C244	0.8
LDTP02205	Tubulin beta chain (TUBB)				C354	0.8
LDTP06366	Poly(rC)-binding protein 1 (PCBP1)				C194	0.7
LDTP13705	LIM and calponin homology domains-containing protein 1 (LIMCH1)				C140	0.7
LDTP10700	KH domain-containing RNA-binding protein QKI (QKI)				C35	0.7
LDTP00431	Kinetochore protein NDC80 homolog (NDC80)				C449	0.6
LDTP04028	DNA mismatch repair protein Msh2 (MSH2)				C843	0.6
LDTP13925	Nucleolar protein 58 (NOP58)				C106	0.6
LDTP09821	Stalled ribosome sensor GCN1 (GCN1)				C1692	0.6
LDTP05021	Large ribosomal subunit protein eL30 (RPL30)				C92	0.4
LDTP01299	WD repeat and HMG-box DNA-binding protein 1 (WDHD1)				C773	0.4

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.