Table I. Proteins recovered by CBX-TAP from HeLa cells.

Bait	Experiment	Accessiona	Protein description	Mass (Da)	Scoreb	Petidesc
CBX2	Exp. 1	ANR26_HUMAN	Ankyrin repeat domain-containing protein 26	196202	39	2
CBX2	Exp. 2	BMI1_HUMAN	Polycomb complex protein BMI-1	36925	201	4
CBX2	Exp. 1/Exp. 2	CBX2_HUMAN	Chromobox protein homolog 2	56046	583/379	43/26
CBX2	Exp. 2	CENPE_HUMAN	Centromeric protein E	316219	62	6
CBX2	Exp. 1/Exp. 2	CSK21_HUMAN	Casein kinase II subunit α	45115	136/66	2/2
CBX2	Exp. 2	CSK22_HUMAN	Casein kinase II subunit α	41187	94	1
CBX2	Exp. 2	CSK2B_HUMAN	Casein kinase II subunit β	24926	136	3
CBX2	Exp. 2	DI3L2_HUMAN	DIS3-like exonuclease 2	99147	43	2
CBX2	Exp. 2	GTF2I_HUMAN	General transcription factor II-I	112346	211	4
CBX2	Exp. 2	H2A1B_HUMAN	Histone H2A type 1-B	14127	80	6
CBX2	Exp. 2	H2B1C_HUMAN	Histone H2B type 1-C/E/F/G/I	13811	98	4
CBX2	Exp. 2	H4_HUMAN	Histone H4	11360	57	1
CBX2	Exp. 1	IQWD1_HUMAN	Nuclear receptor interaction protein	96292	48	2
CBX2	Exp. 1	JHD2A_HUMAN	JmjC domain-containing histone demethylation protein 2A	147234	49	3
CBX2	Exp. 1	LBA1_HUMAN	Lupus brain antigen 1 homolog	336007	64	3
CBX2	Exp. 1	MYCB2_HUMAN	Probable E3 ubiquitin-protein ligase MYCBP2	509759	39	5
CBX2	Exp. 1	NPM_HUMAN	Nucleophosmin	32555	51	1
CBX2	Exp. 1	PAR12_HUMAN	Poly [ADP-ribose] polymerase 12	79013	44	2
CBX2	Exp. 2	PARP1_HUMAN	Poly [ADP-ribose] polymerase 1	113012	113	2
CBX2	Exp. 2	PHC2_HUMAN	Polyhomeotic-like protein 2	90657	350	7
CBX2	Exp. 1/Exp. 2	PSME3_HUMAN	Proteasome activator complex subunit 3	29488	280/195	5/8
CBX2	Exp. 1/Exp. 2	RING2_HUMAN	E3 ubiquitin-protein ligase RING2	37632	281/429	7/8
CBX2	Exp. 1	RN213_HUMAN	RING finger protein 213	373742	57	5
CBX2	Exp. 1	YD007_HUMAN	Coiled-coil domain-containing protein FLJ25770	127062	41	6
CBX2	Exp. 1	ZN167_HUMAN	Zinc finger protein 167	84979	48	2
CBX4	Exp. 1/Exp. 2	1433B_HUMAN	14-3-3 protein β/α	28065	154/329	8/21
CBX4	Exp. 1/Exp. 2	1433E_HUMAN	14-3-3 protein ϵ	29155	566/1151	25/97
CBX4	Exp. 1/Exp. 2	1433F_HUMAN	14-3-3 protein η	28201	79/670	2/42
CBX4	Exp. 1/Exp. 2	1433G_HUMAN	14-3-3 protein γ	28285	188/467	8/36
CBX4	Exp. 2	1433S_HUMAN	14-3-3 protein σ	27757	151	7
CBX4	Exp. 1/Exp. 2	1433T_HUMAN	14-3-3 protein θ	27747	182/600	9/20
CBX4	Exp. 1/Exp. 2	1433Z_HUMAN	14-3-3 protein ζ/Δ	27728	254/572	10/44
CBX4	Exp. 1	ADT2_HUMAN	ADP/ATP translocase 2	32874	143	3
CBX4	Exp. 1/Exp. 2	BMI1_HUMAN	Polycomb complex protein BMI-1	36925	212/337	7/18
CBX4	Exp. 1/Exp. 2	CBX4_HUMAN	E3 SUMO-protein ligase CBX4	61190	266/641	66/137
CBX4	Exp. 2	CENPF_HUMAN	Centromere protein F	367537	46	4
CBX4	Exp. 2	CHD7_HUMAN	Chromodomain-helicase-DNA-binding protein 7	335717	42	4
CBX4	Exp. 1	CSK21_HUMAN	Casein kinase II subunit α	45115	169	3
CBX4	Exp. 1	CSK22_HUMAN	Casein kinase II subunit α	41187	46	1
CBX4	Exp. 1/Exp. 2	CSK2B_HUMAN	Casein kinase II subunit β	24926	59/107	1/2
CBX4	Exp. 1	DDEF1_HUMAN	130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein	125393	49	2
CBX4	Exp. 2	ERCC6_HUMAN	DNA excision repair protein ERCC-6	168416	43	3
CBX4	Exp. 2	FER_HUMAN	Proto-oncogene tyrosine-protein kinase FER	94638	64	2
CBX4	Exp. 1	H11_HUMAN	Histone H1.1	21829	41	4
CBX4	Exp. 2	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal transduction-associated protein 2	38927	46	2
CBX4	Exp. 2	KI67_HUMAN	Antigen KI-67	358474	60	4
CBX4	Exp. 2	MDM1_HUMAN	Nuclear protein MDM1	80686	41	2
CBX4	Exp. 1	MOV10_HUMAN	Putative helicase MOV-10	113599	44	1
CBX4	Exp. 1/Exp. 2	PCGF2_HUMAN	Polycomb group RING finger protein 2	37764	104/143	3/12
CBX4	Exp. 1/Exp. 2	PCGF6_HUMAN	Polycomb group RING finger protein 6	39023	63/78	1/1
CBX4	Exp. 1	PHC1_HUMAN	Polyhomeotic-like protein 1	105353	40	1
CBX4	Exp. 1/Exp. 2	PHC2_HUMAN	Polyhomeotic-like protein 2	90657	141/628	4/19
CBX4	Exp. 1	PHC3_HUMAN	Polyhomeotic-like protein 3	106096	103	4
CBX4	Exp. 1/Exp. 2	RING1_HUMAN	E3 ubiquitin-protein ligase RING1	42403	345/379	12/8
CBX4	Exp. 1/Exp. 2	RING2_HUMAN	E3 ubiquitin-protein ligase RING2	37632	284/598	7/19
CBX4	Exp. 2	RNF17_HUMAN	RING finger protein 17	184643	43	2
CBX4	Exp. 2	RUVB2_HUMAN	RuvB-like 2	51125	84	2
CBX4	Exp. 1	SMC3_HUMAN	Structural maintenance of chromosomes protein 3	141454	61	5
CBX4	Exp. 1	SMG1_HUMAN	Serine/threonine-protein kinase SMG1	410261	46	3
CBX4	Exp. 2	SSX10_HUMAN	Protein SSX10	17575	42	2
CBX4	Exp. 1	STALP_HUMAN	AMSH-like protease	49783	38	2
CBX4	Exp. 2	WDHD1_HUMAN	WD repeat and HMG-box DNA-binding protein 1	125888	41	4
CBX4	Exp. 2	YD007_HUMAN	Coiled-coil domain-containing protein FLJ25770	127062	38	3
CBX4	Exp. 1	YR010_HUMAN	Putative uncharacterized protein ENSP00000344348	46232	42	3
CBX4	Exp. 2	ZN546_HUMAN	Zinc finger protein 546	98369	40	2
CBX6	Exp. 2	AHDC1_HUMAN	A.T hook DNA-binding motif-containing protein 1	168245	41	3
CBX6	Exp. 2	BPTF_HUMAN	Nucleosome-remodeling factor subunit BPTF	324019	49	3
CBX6	Exp. 2	BRWD1_HUMAN	Bromodomain and WD repeat-containing protein 1	262756	40	3
CBX6	Exp. 2	CAF1A_HUMAN	Chromatin assembly factor 1 subunit A	105223	47	2
CBX6	Exp. 2	CASC5_HUMAN	Protein CASC5	265193	43	5
CBX6	Exp. 1/Exp. 2	CBX6_HUMAN	Chromobox protein homolog 2	43871	375/572	72/96
CBX6	Exp. 2	CD014_HUMAN	Uncharacterized protein C4orf14	78409	64	1
CBX6	Exp. 2	CE350_HUMAN	Centrosome-associated protein 350	350716	46	3
CBX6	Exp. 1	CP135_HUMAN	Centrosomal protein of 135 kDa	133422	43	2
CBX6	Exp. 2	DACT1_HUMAN	Dapper homolog 1	90119	48	2
CBX6	Exp. 2	DNMT1_HUMAN	DNA (cytosine-5)-methyltransferase 1	183050	45	3
CBX6	Exp. 2	ELP4_HUMAN	Elongator complex protein 4	46588	59	3
CBX6	Exp. 2	ESF1_HUMAN	ESF1 homolog	98735	69	1
CBX6	Exp. 2	GNL3_HUMAN	Guanine nucleotide-binding protein-like 3	61958	107	3
CBX6	Exp. 2	H12_HUMAN	Histone H1.2	21352	45	1
CBX6	Exp. 2	H14_HUMAN	Histone H1.4	21852	44	2
CBX6	Exp. 2	H1X_HUMAN	Histone H1x	22474	50	1
CBX6	Exp. 2	H2A1B_HUMAN	Histone H2A type 1-B	14127	43	1
CBX6	Exp. 2	H2B1B_HUMAN	Histone H2B type 1-B	13942	118	2
CBX6	Exp. 2	H31T_HUMAN	Histone H3.1t	15499	47	3
CBX6	Exp. 1/Exp. 2	H4_HUMAN	Histone H4	11360	68/54	1/1
CBX6	Exp. 2	IF2B1_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 1	63417	576	15
CBX6	Exp. 2	IF2B2_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 1	61804	89	3
CBX6	Exp. 1/Exp. 2	IF2B3_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 1	63681	322/39	8/1
CBX6	Exp. 2	ILF2_HUMAN	Interleukin enhancer-binding factor 2	43035	284	4
CBX6	Exp. 2	ILF3_HUMAN	Interleukin enhancer-binding factor 3	95279	162	4
CBX6	Exp. 2	KHDR1_HUMAN	KH domain-containing, RNA-binding, signal transduction-associated protein 1	48197	49	3
CBX6	Exp. 2	KRI1_HUMAN	Protein KRI1 homolog	83201	224	4
CBX6	Exp. 2	LA_HUMAN	Lupus La protein	46808	88	1
CBX6	Exp. 2	LAS1L_HUMAN	LAS1-like protein	83013	126	2
CBX6	Exp. 2	LTV1_HUMAN	Protein LTV1 homolog	54821	93	3
CBX6	Exp. 2	MOV10_HUMAN	Putative helicase MOV-10	113599	254	6
CBX6	Exp. 2	MPPH1_HUMAN	M-phase phosphoprotein 1	210553	49	7
CBX6	Exp. 2	NCOR2_HUMAN	Nuclear receptor corepressor 2	274034	49	4
CBX6	Exp. 2	NUCL_HUMAN	Nucleolin	76568	238	4
CBX6	Exp. 2	NUMA1_HUMAN	Nuclear mitotic apparatus protein 1	238260	45	2
CBX6	Exp. 2	PABP1_HUMAN	Polyadenylate-binding protein 1	70626	155	3
CBX6	Exp. 2	PHC2_HUMAN	Polyhomeotic-like protein 2	90657	61	1
CBX6	Exp. 2	PPR3A_HUMAN	Protein phosphatase 1 regulatory subunit 3A	125759	52	3
CBX6	Exp. 2	RAD17_HUMAN	Cell cycle checkpoint protein RAD17	77006	41	2
CBX6	Exp. 2	RAD26_HUMAN	Putative DNA repair and recombination protein RAD26-like	81094	42	2
CBX6	Exp. 2	RGAG1_HUMAN	Retrotransposon gag domain-containing protein 1	144280	58	2
CBX6	Exp. 1	RING1_HUMAN	E3 ubiquitin-protein ligase RING1	42403	73	1
CBX6	Exp. 2	RING2_HUMAN	E3 ubiquitin-protein ligase RING2	37632	91	2
CBX6	Exp. 2	SCML2_HUMAN	Sex comb on midleg-like protein 2	77257	40	3
CBX6	Exp. 2	THOC4_HUMAN	THO complex subunit 4	26872	64	1
CBX6	Exp. 2	UBE2O_HUMAN	Ubiquitin-conjugating enzyme E2 O	141265	221	5
CBX6	Exp. 2	ULK2_HUMAN	Serine/threonine-protein kinase ULK2	112654	41	3
CBX6	Exp. 2	WD40C_HUMAN	WD repeat-containing protein 40C	50803	45	4
CBX6	Exp. 1/Exp. 2	YBOX1_HUMAN	Nuclease-sensitive element-binding protein 1	35903	237/127	8/3
CBX6	Exp. 2	YC009_HUMAN	Uncharacterized protein FLJ36157	190890	52	3
CBX6	Exp. 2	ZMYM4_HUMAN	Zinc finger MYM-type protein 4	172677	43	3
CBX6	Exp. 1/Exp. 2	ZN33A_HUMAN	Zinc finger protein 33A	94384	45/42	3/3
CBX6	Exp. 2	ZN33B_HUMAN	Zinc finger protein 33B	90683	60	3
CBX7	Exp. 1/Exp. 2	BMI1_HUMAN	Polycomb complex protein BMI-1	36925	199/100	4/3
CBX7	Exp. 1/Exp. 2	CBX7_HUMAN	Chromobox protein homolog 7	28323	232/55	10/1
CBX7	Exp. 2	CSK21_HUMAN	Casein kinase II subunit α	45115	255	3
CBX7	Exp. 2	CSK2B_HUMAN	Casein kinase II subunit β	24926	103	2
CBX7	Exp. 1/Exp. 2	PCGF2_HUMAN	Polycomb group RING finger protein 2	37764	75/47	4/2
CBX7	Exp. 1/Exp. 2	PCGF6_HUMAN	Polycomb group RING finger protein 6	39023	95/56	2/3
CBX7	Exp. 1/Exp. 2	PHC2_HUMAN	Polyhomeotic-like protein 2	90657	111/66	3/2
CBX7	Exp. 1	RAD17_HUMAN	Cell cycle checkpoint protein RAD17	77055	45	2
CBX7	Exp. 1/Exp. 2	RING1_HUMAN	E3 ubiquitin-protein ligase RING1	42403	384/334	8/7
CBX7	Exp. 1/Exp. 2	RING2_HUMAN	E3 ubiquitin-protein ligase RING2	37632	627/571	15/12
CBX7	Exp. 1	SPEC1_HUMAN	Sperm antigen with calponin homology and coiled-coil domains 1	118512	48	3
CBX7	Exp. 2	SRBD1_HUMAN	S1 RNA-binding domain-containing protein 1	111705	39	3
CBX7	Exp. 1	TPR_HUMAN	Nucleoprotein TPR	267293	45	3
CBX7	Exp. 2	UBE4A_HUMAN	Ubiquitin conjugation factor E4 A	122561	41	2
CBX7	Exp. 2	UBP20_HUMAN	Ubiquitin carboxyl-terminal hydrolase 20	101938	46	1
CBX7	Exp. 2	WDR68_HUMAN	WD repeat-containing protein 68	38901	41	2
CBX8	Exp. 2	BCLF1_HUMAN	Bcl-2-associated transcription factor 1	106059	84	2
CBX8	Exp. 1/Exp. 2	BMI1_HUMAN	Polycomb complex protein BMI-1	36925	154/122	9/13
CBX8	Exp. 1/Exp. 2	CBX8_HUMAN	Chromobox protein homolog 8	43369	866/803	217/143
CBX8	Exp. 1/Exp. 2	CSK21_HUMAN	Casein kinase II subunit α	45115	63/236	1/6
CBX8	Exp. 1/Exp. 2	CSK2B_HUMAN	Casein kinase II subunit β	24926	76/111	2/2
CBX8	Exp. 1/Exp. 2	DBPA_HUMAN	DNA-binding protein A	40066	213/218	8/4
CBX8	Exp. 2	DGKZ_HUMAN	Diacylglycerol kinase ζ	124044	67	5
CBX8	Exp. 1	DIMT1_HUMAN	Probable dimethyladenosine transferase	35214	253	4
CBX8	Exp. 2	DNL3_HUMAN	DNA ligase 3	102625	44	6
CBX8	Exp. 2	EP300_HUMAN	Histone acetyltransferase p300	263973	43	2
CBX8	Exp. 2	ESCO2_HUMAN	N-acetyltransferase ESCO2	68264	58	2
CBX8	Exp. 2	FBRL_HUMAN	rRNA 2′-O-methyltransferase fibrillarin	33763	94	2
CBX8	Exp. 1	GBLP_HUMAN	Guanine nucleotide-binding protein subunit beta-2-like 1	35055	110	2
CBX8	Exp. 1/Exp. 2	H2A1B_HUMAN	Histone H2A type 1-B	14127	62/42	2/1
CBX8	Exp. 2	H2B1A_HUMAN	Histone H2B type 1-A	14159	40	2
CBX8	Exp. 1/Exp. 2	H2B1B_HUMAN	Histone H2B type 1-B	13942	116/85	2/2
CBX8	Exp. 1/Exp. 2	H4_HUMAN	Histone H4	11360	143/66	6/4
CBX8	Exp. 1/Exp. 2	HLF_HUMAN	Hepatic leukemia factor	33199	59/40	3/3
CBX8	Exp. 1/Exp. 2	IF2B1_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 1	63417	365/169	6/6
CBX8	Exp. 1/Exp. 2	IF2B2_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 2	61804	65/46	2/1
CBX8	Exp. 2	IF2B3_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 3	63681	49	2
CBX8	Exp. 1/Exp. 2	ILF2_HUMAN	Interleukin enhancer-binding factor 2	43035	381/65	7/2
CBX8	Exp. 1/Exp. 2	ILF3_HUMAN	Interleukin enhancer-binding factor 3	95279	146/76	2/2
CBX8	Exp. 2	JIP4_HUMAN	C-jun-amino-terminal kinase-interacting protein 4	146115	48	2
CBX8	Exp. 2	K0020_HUMAN	Pumilio domain-containing protein KIAA0020	73538	47	1
CBX8	Exp. 1/Exp. 2	KRI1_HUMAN	Protein KRI1 homolog	83201	241/100	4/1
CBX8	Exp. 2	KRR1_HUMAN	KRR1 small subunit processome component homolog	43638	91	2
CBX8	Exp. 2	LTV1_HUMAN	Protein LTV1 homolog	54821	127	3
CBX8	Exp. 1	MK67I_HUMAN	MKI67 FHA domain-interacting nucleolar phosphoprotein	34201	67	1
CBX8	Exp. 1/Exp. 2	MOV10_HUMAN	Putative helicase MOV-10	113599	364/268	9/6
CBX8	Exp. 2	MPPH1_HUMAN	M-phase phosphoprotein 1	210553	42	3
CBX8	Exp. 2	NBN_HUMAN	Nibrin	84906	48	2
CBX8	Exp. 2	NCOAT_HUMAN	Bifunctional protein NCOAT	102849	59	4
CBX8	Exp. 2	NFIL3_HUMAN	Nuclear factor interleukin-3-regulated protein	51472	53	2
CBX8	Exp. 1	NOG1_HUMAN	Nucleolar GTP-binding protein 1	73918	71	2
CBX8	Exp. 1/Exp. 2	NOL1_HUMAN	Putative RNA methyltransferase NOL1	89247	105/62	2/1
CBX8	Exp. 2	NPM_HUMAN	Nucleophosmin	32555	165	4
CBX8	Exp. 1	NSBP1_HUMAN	Nucleosome-binding protein 1	31525	47	2
CBX8	Exp. 1/Exp. 2	NUCL_HUMAN	Nucleolin	76568	376/287	10/10
CBX8	Exp. 2	PCGF1_HUMAN	Polycomb group RING finger protein 1	29202	54	3
CBX8	Exp. 1/Exp. 2	PCGF2_HUMAN	Polycomb group RING finger protein 2	37764	110/59	4/2
CBX8	Exp. 2	PCGF3_HUMAN	Polycomb group RING finger protein 3	28097	58	1
CBX8	Exp. 2	PCGF5_HUMAN	Polycomb group RING finger protein 5	29694	50	2
CBX8	Exp. 1/Exp. 2	PCGF6_HUMAN	Polycomb group RING finger protein 6	39023	136/42	3/1
CBX8	Exp. 1/Exp. 2	PHC2_HUMAN	Polyhomeotic-like protein 2	90657	192/53	3/1
CBX8	Exp. 1	RING1_HUMAN	E3 ubiquitin-protein ligase RING1	42403	124	3
CBX8	Exp. 1/Exp. 2	RING2_HUMAN	E3 ubiquitin-protein ligase RING2	37632	395/346	11/11
CBX8	Exp. 1/Exp. 2	RRP5_HUMAN	Protein RRP5 homolog	208570	272/61	11/1
CBX8	Exp. 2	SETD2_HUMAN	Histone-lysine N-methyltransferase SETD2	287550	47	5
CBX8	Exp. 1	SSF1_HUMAN	Suppressor of SWI4 1 homolog	53161	66	2
CBX8	Exp. 1	STAU1_HUMAN	Double-stranded RNA-binding protein Staufen homolog 1	63143	113	2
CBX8	Exp. 1/Exp. 2	THOC4_HUMAN	THO complex subunit 4	26872	98/65	2/1
CBX8	Exp. 1/Exp. 2	TSR1_HUMAN	Pre-rRNA-processing protein TSR1 homolog	91752	100/92	2/2
CBX8	Exp. 2	UBR1_HUMAN	E3 ubiquitin-protein ligase UBR1	200080	62	3
CBX8	Exp. 1/Exp. 2	YBOX1_HUMAN	Nuclease-sensitive element-binding protein 1	35903	339/204	11/7
CBX8	Exp. 1	YTDC2_HUMAN	YTH domain-containing protein 2	74853	98	2
CBX8	Exp. 2	ZCHC3_HUMAN	Zinc finger CCHC domain-containing protein 3	43591	86	2
CBX8	Exp. 1/Exp. 2	ZFR_HUMAN	Zinc finger RNA-binding protein	116939	115/39	2/1
CBX8	Exp. 2	ZN717_HUMAN	Zinc finger protein 717	105183	46	3
CBX8	Exp. 1	ZN828_HUMAN	Zinc finger protein 828	89099	51	3

^a SWISS PROTEIN data base accession.

^b Mascot protein score.

^c Number of different peptides.