. 2012 Nov;86(21):11567–11580. doi: 10.1128/JVI.00456-12

Table 1.

Viral content of BoHV-4 extracellular virions^a

ORF	Protein description	Predicted MM (kDa)	pK^b	2D gel/nano-LC-MS/MS					1D gel/nano-LC-MS/MS					Deglyco-1D gel/nano-LC-MS/MS
ORF	Protein description	Predicted MM (kDa)	pK^b	No. of peptides	Prot matches	Coverage (%)	emPAI	emPAI (%)	No. of peptides	Prot matches	Coverage (%)	emPAI	emPAI (%)	No. of peptides	Prot matches	Coverage (%)	emPAI	emPAI (%)
ORF3	BORFA1; v-FGAM-synthase	144.18	+	16	21	0.18	0.54	2.21	17	76	0.20	0.62	0.71	8	11	0.10	0.22	0.69
ORF6	Single-stranded DNA-binding protein MDBP	129.68	–	2	2	0.03	0.06	0.25	1	1	0.01	0.03	0.03
ORF8	Glycoprotein B	100.08	+	21	33	0.31	1.48	6.05	25	110	0.37	3.11	3.55	21	84	0.30	1.97	6.22
Bo5	Homolog of KSHV K5-encoded E3 ubiquitin ligase	35.48	–	4	6	0.20	0.65	2.66
ORF16	v-Bcl-2 protein	26.06	–	1	1	0.10	0.15	0.61	1	1	0.04	0.15	0.17
ORF17	Minor scaffold protein (protease)	57.74	+	9	23	0.22	1.25	5.11	9	47	0.22	1.25	1.43	5	9	0.13	0.37	1.17
ORF19	Capsid vertex-specific complex protein (CVSC)	63.39	+	5	6	0.15	0.33	1.35	7	14	0.16	0.49	0.56	1	1	0.02	0.06	0.19
ORF22	Glycoprotein H	82.23	+	6	8	0.11	0.3	1.23	13	54	0.25	0.94	1.07	13	38	0.26	0.94	2.97
ORF25	Major capsid protein	155.12	+	56	296	0.58	8.52	34.80	63	1208	0.60	13.88	15.86	51	480	0.54	7.27	22.94
ORF26	Triplex component	34.3	+	8	26	0.39	1.84	7.52	12	155	0.56	5.53	6.32	11	57	0.54	5.53	17.45
ORF32	Viral DNA cleavage/packaging protein (CVSC)	59.9	+	3	3	0.10	0.23	0.94	6	28	0.19	0.72	0.82	3	6	0.10	0.23	0.73
ORF33	Tegument protein	39.36	+	7	16	0.36	1.07	4.37	13	107	0.47	3.7	4.23	7	48	0.33	1.48	4.67
ORF36	Kinase	45.16	–						1	1	0.04	0.08	0.09
ORF38	Myristylated tegument protein	7.7	+						1	1	0.50	0.54	0.62	1	1	0.50	0.54	1.70
ORF39	Glycoprotein M	43.36	+	3	4	0.15	0.28	1.14	1	20	0.04	0.09	0.10	1	8	0.04	0.09	0.28
ORF42	Potential tegument protein (UL7 homolog)	33.65	+											1	1	0.06	0.11	0.35
ORF43	Portal protein	71.11	+	3	5	0.09	0.16	0.65	2	6	0.05	0.11	0.13
ORF45	Tegument protein, IRF-7 blocking protein	27.18	+	8	21	0.37	3.21	13.11	9	36	0.48	3.21	3.67	4	11	0.25	0.69	2.18
ORF46	Uracil DNA glycosylase	29.07	–						1	1	0.04	0.13	0.15
ORF47	Glycoprotein L	16.28	–	2	2	0.20	0.53	2.17	1	4	0.06	0.24	0.27	1	1	0.06	0.24	0.76
ORF48		59.17	+	11	18	0.32	1.21	4.94	13	79	0.36	1.82	2.08	14	59	0.34	1.65	5.21
Bo10	Glycoprotein gp180	28.51	+	1	1	0.05	0.13	0.53	2	12	0.08	0.45	0.51	3	6	0.12	0.45	1.42
ORF52	Tegument protein	13.85	+	7	103	0.55	24.48	100.0	8	140	0.55	87.53	100.0	6	61	0.55	31.69	100.0
ORF54	dUTPase	31.14	–						1	1	0.06	0.12	0.14
ORF55	Tegument protein (UL51 homolog)	22.23	+											2	4	0.14	0.37	1.17
ORF57	Posttranscriptional regulatory protein	48.17	–											1	1	0.04	0.08	0.25
ORF59	DNA replication protein	44.06	–	6	8	0.22	0.77	3.15	7	12	0.24	0.77	0.88	3	7	0.12	0.39	1.23
ORF60	Ribonucleotide reductase small subunit	35.65	–						1	1	0.04	0.11	0.13
ORF62	Capsid triplex component	38.71	+	6	17	0.22	1.1	4.49	11	74	0.38	3.39	3.87	8	27	0.25	1.77	5.59
ORF63	Tegument protein	109	+	5	6	0.08	0.18	0.74	18	30	0.26	0.95	1.09	6	11	0.10	0.22	0.69
ORF64	Tegument protein	288.8	+	11	15	0.08	0.18	0.74	37	77	0.19	0.64	0.73	1	1	0.01	0.01	0.03
ORF65	Small capsomer interacting protein	14.61	+	1	1	0.11	0.27	1.10	2	15	0.35	1.58	1.81	1	4	0.25	0.61	1.92
ORF67	Tegument protein	30.33	–						2	2	0.13	0.27	0.31
ORF75	v-FGAM-synthase	125.3	+	18	25	0.22	0.64	2.61	23	122	0.29	1.19	1.36	22	95	0.27	1.25	3.94

2D gel/nano-LC-MS/MS and 1D gel/nano-LC-MS/MS were accomplished in technical replicates, and the results were pooled. The “number of peptides” indicates the number of unique peptides identified per protein. “Prot matches” indicates the number of peptides detected per protein. “Coverage” indicates the percentages of coverage of proteins by peptides. emPAI values were calculated as described by Ishihama et al. (24). Relative emPAI values [emPAI (%)] were calculated as percentages of the pORF52 maximum abundance.

pK, proteinase K treatment. +, Proteins detected in the proteinase K–1D gel/nano-LC-MS/MS.