. 2014 Sep;88(17):9633–9646. doi: 10.1128/JVI.01415-14

TABLE 3.

Fifty most abundant cellular proteins detected by nanoscale UPLC-MS in virion preparations from pp65pos and pp65neg strains

Description	Maximum score^a	No. of reported peptides^b	Copy no.^c				Relative copy no. ratio^d
Description	Maximum score^a	No. of reported peptides^b	BADwt	KB14	HB5	Hd65	Hd65/HB5	KB14/BADwt
Keratin type II cytoskeletal 2 epidermal (KRT2)	33,702	38	0.1717	0.0095	0.0052	0.0033	0.64	0.06
Myosin 9 (MYH9)	1,605	59	0.1505	0.1121	0.1075	0.1485	1.38	0.75
Keratin type I cytoskeletal 10 (KRT10)	38,102	30	0.1501	0.0191	0.0066	0.0057	0.86	0.13
Actin cytoplasmic 1 (ACTB)	48,610	23	0.0933	0.2005	0.1176	0.0719	0.61	2.15
Heat shock cognate 71-kDa protein (HSPA8)	31,490	35	0.0861	0.0591	0.0574	0.0394	0.69	0.69
Keratin type II cytoskeletal 1 (KRT1)	23,636	35	0.0702	0.0310	0.0247	0.0097	0.39	0.44
Elongation factor 1 alpha 1 (EEF1A1)	17,000	20	0.0662	0.0975	0.0576	0.0460	0.80	1.47
Serum albumin (ALB)	7,336	21	0.0532	0.0411	0.0500	0.0288	0.58	0.77
Glyceraldehyde 3 phosphate dehydrogenase (GAPDH)	33,212	21	0.0526	0.1042	0.0741	0.0385	0.52	1.98
Keratin type I cytoskeletal 17 (KRT17)	3,539	20	0.0482	0.0298	0.0345	0.0530	1.54	1.44
Peptidyl prolyl cis trans isomerase A (PPIA)	30,655	12	0.0454	0.0338	0.0258	0.0344	1.33	0.75
26S protease regulatory subunit 6A (PSMC30)	1,023	5	0.0392	0.0249	0.0191	0.0742	3.89	0.64
Ras-related protein Rab 43 (RAB43)	2,637	4	0.0356	0.0076	0.0262	0.0096	0.37	0.21
Thioredoxin (TXN)	30,652	6	0.0304	0.0257	0.0195	0.0253	1.30	0.85
Annexin A2 (ANXA2)	18,059	29	0.0289	0.0270	0.0266	0.0205	0.77	0.93
Putative heat shock protein HSP 90 beta 4 (HSP90AB4P)	2,807	8	0.0239	0.0002	0.0094	0.0003	0.03	0.008
Keratin type II cytoskeletal 1b (KRT77)	3,266	14	0.0235	0.0067	0.0132	0.0115	0.87	0.29
Profilin 1 (PFN1)	24,876	8	0.0234	0.0260	0.0212	0.0174	0.82	1.11
Actin gamma enteric smooth muscle (ACTG2)	22,060	16	0.0227	0.0232	0.0138	0.0149	1.08	1.02
Phosphatidylinositol 4 phosphate 3 kinase C2 domain-containing subunit alpha (PIK3)	796	48	0.0194	0.0173	0.0154	0.0228	1.48	0.89
E3 ubiquitin protein ligase TRIM63 (TRIM63)	889	5	0.0193	0.0174	0.0146	0.0152	1.04	0.90
Keratin type I cytoskeletal 19 (KRT19)	4,111	12	0.0193	0.0055	0.0171	0.0091	0.53	0.29
Peripherin (PRPH)	938	7	0.0176	0.0133	0.0120	0.0316	2.63	0.76
E3 SUMO protein ligase RanBP2 (RANBP2)	969	51	0.0175	0.0031	0.0187	0.0055	0.24	0.18
14-3-3 protein epsilon (YWHAE)	28,144	20	0.0173	0.0273	0.0109	0.0293	2.69	1.58
Heat shock 70-kDa protein 1A 1B (HSPA1A)	13,281	31	0.0171	0.0116	0.0113	0.0091	0.80	0.68
14-3-3 protein zeta delta (YWHAZ)	23,199	17	0.0166	0.0201	0.0113	0.0232	2.05	1.20
Galectin 1 (LGALS1)	32,764	9	0.0160	0.0248	0.0178	0.0131	0.74	1.55
Alpha enolase (ENO1)	13,422	24	0.0155	0.0182	0.0150	0.0086	0.57	1.17
Cofilin 1 (CFL1)	19,199	13	0.0149	0.0181	0.0155	0.0089	0.57	1.22
Tubulin beta chain (TUBB)	25,232	22	0.0145	0.0250	0.0125	0.0098	0.78	1.74
Keratin type I cuticular Ha6 (KRT36)	1,115	9	0.0145	0.0009	0.0068	0.0011	0.16	0.06
Complement decay-accelerating factor (CD55)	3,887	15	0.0143	0.0084	0.0123	0.0103	0.84	0.59
Keratin type I cytoskeletal 28 (KRT28)	2,847	13	0.0140	0.0012	0.0119	0.0028	0.24	0.09
ADP ribosylation factor 1 (ARF1)	17,453	11	0.0140	0.0082	0.0139	0.0098	0.71	0.59
Pyruvate kinase isozymes M1 M2 (PKM2)	14,429	32	0.0132	0.0214	0.0182	0.0099	0.54	1.60
CD81 antigen (CD81)	5,301	4	0.0121	0.0088	0.0095	0.0119	1.25	0.72
Cell division control protein 42 homolog (CDC42)	4,853	6	0.0119	0.0035	0.0084	0.0032	0.38	0.29
Tubulin beta 8 chain B OS Homo sapiens	1,482	8	0.0118	0.0003	0.0071	0.0002	0.03	0.03
14 3 3 protein theta (YWHAQ)	17,722	16	0.0118	0.0183	0.0087	0.0210	2.97	1.55
Elongation factor 2 (EEF2)	7,846	38	0.0117	0.0129	0.0126	0.0075	0.59	1.10
Staphylococcal nuclease domain-containing protein 1 (SND1)	934	31	0.0116	0.0040	0.0050	0.0029	0.58	0.35
Tubulin alpha 1A chain (TUBA1A)	19,169	24	0.0116	0.0213	0.0141	0.0094	0.66	1.84
Tubulin alpha 1C chain (TUBA1C)	19,614	23	0.0115	0.0272	0.0110	0.0074	0.67	2.37
Tryptophanyl tRNA synthetase cytoplasmic (WARS)	453	7	0.0111	0.0108	0.0123	0.0090	0.73	0.97
Lactadherin (MFGE8)	6,952	21	0.0108	0.0064	0.0071	0.0079	1.11	0.59
Probable phosphoglycerate mutase 4 (PGAM4)	1,867	4	0.0106	0.0126	0.0031	0.0112	3.61	1.19
Keratin type II cytoskeletal 5 (KRT5)	8,085	24	0.0105	0.0041	0.0044	0.0078	1.77	0.39
Keratin type II cytoskeletal 2 oral (KRT76)	7,435	9	0.0103	0.0009	0.0011	0.0003	0.27	0.09
Protein S100 A6 (S100A6)	3,706	3	0.0101	0.0101	0.0103	0.0073	0.71	1.00

Maximum PLGS identification score; Tandem MS Search Algorithm (Waters).

Number of peptides detected for each protein.

Calculated copy numbers of molecules per MCP molecule.

Ratios of the relative copy numbers of individual proteins (pp65neg versus pp65pos strains). The proteins are listed according to decreasing frequencies in virions of RV-BADwt. Ratios of more than 2.0 and less than 0.5 are indicated by boldface.