TABLE 1.
Database of identified proteins
| Protein | GenBank accession no. | Identification code | No. of peptidesb | Sequence coverage (%)b | No. of MS/MSb | Plate | Fraction(s)a | Scoreb |
|---|---|---|---|---|---|---|---|---|
| BVD proteins | ||||||||
| Envelope protein p57 precursor (G) | P52638 | VGLG_BDV | 1 | 1.6 | 2 | 3 | 17 (13-14) | 52.63 |
| Matrix protein (M) | P52637 | MATRX_BDV | 5 | 35.9 | 8 | 1 | 10 (19); 11 (19) | 111.54 |
| Matrix protein (M) | P52637 | MATRX_BDV | 2 | 17.6 | 8 | 2 | 13 (19-20); 14 (18-19); 15 (19) | 89.69 |
| Matrix protein (M) | P52637 | MATRX_BDV | 3 | 18.3 | 4 | 3 | 17 (19-20); 18 (18) | 73.15 |
| Matrix protein (M) | P52637 | MATRX_BDV | 4 | 26.8 | 5 | 5 | 25 (18) | 92.29 |
| Nucleoprotein (N) | Q01552 | NCAP_BDV | WBd | WBd | WBd | 2 | 16 | WBd |
| Phosphoprotein (P) | P26668 | PHOSP_BDV | 3 | 13.9 | 3 | 4 | 24 (21) | 30.31 |
| X protein | Q912Z9 | X_BDV | 1 | 9.2 | 1 | 1 | 9 (12); 11 (12) | 44.01 |
| Proteins involved in neurotransmission and neurogenesis | ||||||||
| AH receptor-interacting protein (AIP) | Q5FWY5 | AIP_RAT | 4 | 10.3 | 4 | 3 | 17 (16-17) | 56.76 |
| Alpha-2-macroglobulin receptor-associated precursor (Alpha-2-MRAP) | Q99068 | AMRP_RAT | 41 | 70.3 | 114 | 3 | 18 (14-15) | 939.8 |
| Alpha-2-MRAP | Q99068 | AMRP_RAT | 18 | 52.2 | 27 | 1 | 9 (15-16) | 201.64 |
| Amyloid-like protein 1 precursor (APLP) | Q03157 | APLP1_MOUSE | 6 | 10.9 | 6 | 5 | 31 (15) | 64.66 |
| BASP-1 (NAP22) | Q05175 | BASP_RAT | 3 | 15.9 | 3 | 4 | 23 (9-10) | 60.54 |
| Brain FABP | O15540 | FABPB_HUMANc | 1 | 6.8 | 1 | 4 | 22 (14) | 49.41 |
| Brain FABP | P55051 | FABPB_RAT | 7 | 63.6 | 26 | 1 | 9 (14); 10 (18) | 214.75 |
| Cholecystokinin precursor | P01355 | CCKN_RAT | 4 | 28.7 | 15 | 1 | 9 (11) | 58.58 |
| Complexin 1 | P63040 | CPLX1_MOUSEc | 13 | 70.1 | 41 | 5 | 25 (13-14) | 281.14 |
| Dihydropyrimidinase-related protein 5 (DRP-5) (ULIP6 protein) (CRMP-5) | Q9JHU0 | DPYL5_RAT | 3 | 6.9 | 7 | 1 | 11 (11-12) | 108.14 |
| Dihydropyrimidinase-related protein 5 (DRP-5) (ULIP6 protein) (CRMP-5) | Q9JHU0 | DPYL5_RAT | 33 | 51.2 | 146 | 3 | 17 (17-18-19-20) | 572.26 |
| DRP-2 | O02675 | DPYL2_BOVINc | 5 | 7.9 | 25 | 1 | 10 (13) | 172.44 |
| Glutamate dehydrogenase 1 mitochondrial precursor (GDH) | P26443 | DHE3_MOUSEc | 15 | 21.3 | 15 | 1 | 9 (18) | 175.53 |
| Glutamate dehydrogenase 1 mitochondrial precursor (GDH) | P26443 | DHE3_MOUSEc | 18 | 24.7 | 18 | 2 | 16 (18) | 321.84 |
| Glutamine synthetase | P09606 | GLNA_RAT | 16 | 29.2 | 17 | 3 | 17 (16) | 152.79 |
| MARCKS | P30009 | MARCS_RAT | 5 | 18.8 | 5 | 4 | 24 (9-10-11) | 89.83 |
| MARCKS | P30009 | MARCS_RAT | 12 | 55.7 | 24 | 5 | 25 (9-10) | 494.6 |
| MARCKS-related protein 1 | Q9EPH2 | MRP_RAT | 3 | 28.1 | 3 | 4 | 23 (9-10) | 86.02 |
| MSAP (MIR-interacting saposin-like protein) | A0JN30 | A0JN30_RAT | 5 | 28.6 | 5 | 5 | 25 (17) | 124.64 |
| mUNC18 | P61763 | STXB1_BOVINc | 7 | 10.1 | 14 | 4 | 24 (21) | 207.11 |
| Neuromodulin (GAP43) | P07936 | NEUM_RAT | 25 | 89.8 | 156 | 5 | 31 (15) | 2178.44 |
| Neuronal pentraxin receptor | O35764 | NPTXR_RAT | 7 | 13 | 7 | 3 | 17 (17-18) | 113.51 |
| Paralemmin (Palm protein) | Q920Q0 | Q920Q0_RAT | 6 | 15.9 | 6 | 5 | 31 (15) | 132.61 |
| Phosphatidylethanolamine-binding protein 1 | P31044 | PEBP1_RAT | 1 | 7 | 1 | 1 | 9 (13) | 70.45 |
| Proenkephalin A precursor | P22005 | PENK_MOUSEc | 1 | 3.3 | 1 | 5 | 25 (9-10) | 62.61 |
| Secretogranin 2 precursor | P10362 | SCG2_RAT | 5 | 8.4 | 8 | 5 | 25 (13-14) | 75.79 |
| Secretogranin-3 precursor (SgIII) | P47868 | SCG3_RAT | 5 | 12.5 | 5 | 5 | 25 (18) | 87.84 |
| Synapsin 1 | P09951 | SYN1_RAT | 23 | 48.9 | 78 | 1 | 9 (17) | 421.08 |
| Synapsin 1 | P09951 | SYN1_RAT | 6 | 12.2 | 6 | 2 | 16 (17) | 111.25 |
| Synapsin 1 | P09951 | SYN1_RAT | 3 | 4.5 | 3 | 3 | 17 (17-18) | 90.87 |
| VGF nerve growth factor inducible | Q0VGU4 | Q0VGU4_MOUSEc | 4 | 4.9 | 5 | 3 | 20 (11) | 126.26 |
| VGF nerve growth factor inducible | Q0VGU4 | Q0VGU4_MOUSEc | 2 | 5 | 3 | 5 | 31 (15); 25 (9-10) | 88.33 |
| Proteins involved in cytoskeleton dynamics | ||||||||
| Actin-binding LIM protein 1 | Q8K4G5 | ABLM1_MOUSEc | 18 | 26.1 | 63 | 2 | 15 (15); 16(16) | 398.36 |
| Actin-binding LIM protein 1 | Q8K4G5 | Q3KR72_RAT | 5 | 12.9 | 5 | 3 | 17 (16) | 110.85 |
| Arp2/3 complex | Q2LE71 | Q2LE71_HUMAN | 5 | 22.5 | 12 | 2 | 16 (18) | 113.59 |
| Cofilin | P45592 | COF1_RAT | 6 | 46.4 | 12 | 1 | 9 (14) | 154.31 |
| Ezrin-radixin-moesin binding phosphoprotein 50 (EBP50) | Q9JJ19 | NHERF_RAT | 5 | 16 | 5 | 3 | 18 (14-15) | 80.29 |
| EBP50 | P70441 | NHERF_MOUSEc | 4 | 9.3 | 4 | 5 | 25 (13-14) | 41.37 |
| Growth arrest-specific protein 7 (GAS-7) | O55148 | GAS7_RAT | 22 | 37 | 39 | 3 | 17 (16) | 340.59 |
| MAP1B (neuraxin) | P15205 | MAP1B_RAT | 8 | 4.3 | 33 | 3 | 17 (14-15); 18 (18-19) | 260.41 |
| Neuronal migration protein doublecortin (lissencephalin-X) (Lis-X) (doublin) | O43602 | DCX_HUMANc | 4 | 10.2 | 13 | 1 | 11 (15-16-17); 12 (18-19) | 94.64 |
| Platelet-activating factor acetylhydrolase 1B gamma | Q61205 | PA1B3_MOUSEc | 3 | 10.8 | 3 | 3 | 18 (18-19) | 65.26 |
| Platelet-activating factor acetylhydrolase 1B alpha | P43034 | LIS1_HUMANc | 6 | 14.1 | 11 | 2 | 15 (16) | 124.82 |
| Profilin 2 | Q09430 | PROF2_BOVINc | 4 | 23.6 | 6 | 3 | 17 (14-15);17 (19-20) | 78.77 |
| Septin 11 | Q8C1B7 | SEP11_MOUSE | 11 | 25.3 | 28 | 1 | 9 (15-16) | 174.36 |
| Septin 11 | Q8C1B7 | SEP11_MOUSE | 23 | 33.4 | 34 | 2 | 16 (17) | 348.68 |
| Septin 11 | Q8C1B7 | SEP11_MOUSE | 28 | 43.6 | 63 | 3 | 17 (17-18) | 495.88 |
| Septin 8 | Q5SX81 | SEPT8_BOVIN | 10 | 13.6 | 10 | 3 | 17 (17-18) | 44.97 |
| Septin 9 | Q9ZQZR6 | SEPT9_RAT | 6 | 11.3 | 7 | 4 | 21 (16) | 86.04 |
| Stathmin | P13668 | STMN1_RAT | 7 | 40.3 | 65 | 1 | 9 (15-16) | 151.23 |
| Stathmin | P13668 | STMN1_RAT | 21 | 67.8 | 82 | 4 | 24 (9-10-11) | 450.18 |
| STOP protein | Q63560 | Q63560_RAT | 26 | 33.7 | 145 | 1 | 9 (14); 12 (12-13) | 685.15 |
| Proteins involved in regulation of mRNA localization | ||||||||
| ELAV-like protein 3 (Hu-antigen C) (HuC) | Q60900 | ELAV3_MOUSEc | 3 | 7.1 | 7 | 1 | 10 (17-18-19) | 59.5 |
| Lupus La protein homolog | P38656 | LA_RAT | 16 | 32.5 | 28 | 1 | 11 (18) | 255.12 |
| Matrin 3 | P43244 | MATR3_RAT | 4 | 3.6 | 5 | 3 | 17 (16) | 44.45 |
| NoNo | Q5FVM4 | NONO_RAT | 35 | 43.3 | 52 | 1 | 9 (18) | 364.94 |
| NoNo | Q15233 | NONO_HUMANc | 13 | 21.7 | 20 | 3 | 17 (17-18) | 54.78 |
| Treacle | O08784 | TCOF_MOUSE | 2 | 1.5 | 2 | 2 | 14 (13-14) | 35.63 |
| Wiskott-Aldrich syndrome protein-interacting protein (WASP-interacting protein) | Q8K1I7 | WIPF1_MOUSE | 2 | 3.9 | 2 | 1 | 12 (10-11) | 43.39 |
| Transcriptional and translational repressors | ||||||||
| MeCP2 | Q00566 | MECP2_RAT | 12 | 25.8 | 12 | 1 | 12 (14; 16) | 245.22 |
| MeCP2 | Q00566 | MECP2_RAT | 25 | 42.1 | 25 | 2 | 13 (14); 14 (13-14) | 410.03 |
| Nuclease-sensitive element-binding protein 1 (YB1) | P62960 | YBOX1_MOUSEc | 23 | 67.1 | 186 | 1 | 12 (10-11) | 848.98 |
| Nuclease-sensitive element-binding protein 1 (YB1) | Q3ZAV2 | Q3ZAV2_RAT | 34 | 73 | 100 | 2 | 13 (14); 14 (10-14); 16 (11) | 897.77 |
| Nuclease-sensitive element-binding protein 1 (YB1) | P67808 | YBOX1_BOVINc | 8 | 29.3 | 9 | 4 | 23 (9-10) | 61.37 |
| Histones | ||||||||
| H2A histone family; J member | Q3ZBX9 | Q3ZBX9_BOVIN | 6 | 44.2 | 151 | 2 | 16 (17) | 228.09 |
| Histone cluster 1.H2aj | A2RUU6 | A2RUU6_HUMAN | 8 | 66.4 | 384 | 2 | 13 (17) | 801.24 |
| Histone H2A.x (H2a/x) | P16104 | H2AX_HUMAN | 8 | 63.6 | 91 | 2 | 13 (17) | 183.97 |
| Histone H2A.x (H2a/x) | P27661 | H2AX_MOUSE | 8 | 63.6 | 90 | 2 | 13 (17) | 157.01 |
| Histone H2B (fragment) | Q29574 | Q29574_PIGc | 17 | 66.7 | 277 | 1 | 11 (15-16) | 1149.24 |
| Histone H2B type 1-N | Q32L48 | H2B1N_BOVIN | 13 | 67.5 | 1643 | 1 | 11 (16-17) | 2405.83 |
| Histone H2B | Q3KP43 | Q3KP43_HUMAN | 7 | 63.8 | 92 | 1 | 11 (15) | 449.79 |
| Histone H2B type 1-N | Q32L48 | H2B1N_BOVIN | 12 | 52.4 | 1271 | 2 | 13 (19-20); 16 (11-16) | 1419.12 |
| Histone cluster 1.H2bh | A2RTP6 | A2RTP6_MOUSE | 18 | 73 | 2155 | 2 | 13 (14-16); 14 (15); 15 (16) | 1637.31 |
| Histone H2B (fragment) | Q29574 | Q29574_PIGc | 21 | 79.7 | 187 | 2 | 13 (15); 14 (14-15-16) | 1392.22 |
| Histone H4 (fragment) | A0AUM5 | A0AUM5_MOUSEc | 13 | 62 | 349 | 1 | 11 (18); 12 (16) | 3459.32 |
| Histone H4 | Q9D0C9 | Q9D0C9_MOUSEc | 8 | 60.2 | 28 | 2 | 13 (16) | 509.01 |
| Histone H4 (fragment) | A0AUM5 | A0AUM5_MOUSEc | 17 | 67 | 276 | 2 | 13 (16); 14 (16); 16 (17) | 1404.42 |
| Other proteins | ||||||||
| 60S ribosomal protein L6 (fragment) | Q6P790 | Q6P790_RAT | 20 | 44.1 | 25 | 3 | 18 (14) | 193.28 |
| Aconitate hydratase. mitochondrial | Q9ER34 | ACON_RAT | 39 | 45.1 | 126 | 3 | 17 (17-18) | 775.81 |
| Ataxin-2-like protein | Q8WWM7 | ATX2L_HUMAN | 13 | 12.5 | 13 | 5 | 31 (15) | 113.41 |
| ATP synthase e chain; mitochondrial | P29419 | ATP5I_RAT | 7 | 71.8 | 26 | 2 | 13 (15) | 232.03 |
| ATP synthase e chain; mitochondrial | P29419 | ATP5I_RAT | 5 | 69 | 11 | 3 | 18 (14) | 127.14 |
| ATP synthase f chain; mitochondrial | P56135 | ATPK_MOUSE | 2 | 20.5 | 4 | 2 | 14 (16); 15 (16) | 59.07 |
| ATP synthase alpha chain; mitochondrial precursor | P15999 | ATPA_RAT | 15 | 25.9 | 15 | 3 | 17 (20) | 309.34 |
| ATP synthase subunit O; mitochondrial precursor | Q06647 | ATPO_RAT | 9 | 40.4 | 16 | 2 | 13 (20); 15 (20) | 216.85 |
| BolA-like 2 | Q0P601 | Q0P601_MOUSE | 5 | 51.2 | 11 | 3 | 17 (14) | 130.83 |
| Cyclic AMP-dependent protein kinase inhibitor gamma (PKI-gamma) | Q7YQJ3 | IPKG_BOVINc | 1 | 21.1 | 1 | 5 | 31 (9) | 60.74 |
| Catalase (EC 1.11.1.6) | P04762 | CATA_RAT | 25 | 46.5 | 74 | 2 | 15 (17-18); 16 (17) | 480.78 |
| Chaperonin subunit 6a (zeta) | Q3MHS9 | Q3MHS9_RAT | 19 | 32.8 | 19 | 3 | 17 (21) | 114.72 |
| Cold-inducible RNA-binding protein (CIRP) | P60826 | CIRBP_CRIGRc | 6 | 41.9 | 19 | 1 | 9 (13) | 173.67 |
| Cytochrome c oxidase polypeptide VIIa-liver/heart; mitochondrial precursor | P35171 | CX7A2_RAT | 1 | 12 | 4 | 2 | 13 (16); 14 (16) | 75.48 |
| Eukaryotic translation initiation factor 2beta | Q6P685 | Q6P685_RAT | 16 | 41.1 | 18 | 5 | 31 (9) | 463.48 |
| Heterogeneous nuclear ribonucleoprotein A1 (helix-destabilizing protein) | P09867 | ROA1_BOVINc | 7 | 32.8 | 7 | 3 | 17 (13) | 84.1 |
| Heterogeneous nuclear ribonucleoprotein A1 | P09651 | ROA1_HUMANc | 23 | 41.4 | 116 | 1 | 9 (11-13) | 641.89 |
| Heterogeneous nuclear ribonucleoprotein D0 | Q14103 | HNRPD_HUMANc | 9 | 21.4 | 20 | 4 | 22 (14) | 186.16 |
| Heterogeneous nuclear ribonucleoprotein H | P31943 | HNRH1_HUMAN | 6 | 16 | 15 | 3 | 17 (15) | 125.09 |
| Heterogeneous nuclear ribonucleoprotein Q | O60506 | HNRPQ_HUMANc | 5 | 10 | 7 | 2 | 13 (18) | 115.12 |
| Inorganic pyrophosphatase 2; mitochondrial precursor | Q91VM9 | IPYR2_MOUSE | 8 | 22.4 | 8 | 3 | 18 (15) | 115.17 |
| p21 Ras GTPase-activating protein-associated p62 (Sam68) | Q91V33 | SAM68_RAT | 10 | 29.8 | 10 | 5 | 25 (17) | 116.12 |
| Low-molecular-wt phosphotyrosine protein phosphatase (LMW-PTP) | P41498 | PPAC_RAT | 6 | 41.1 | 15 | 3 | 18 (14-15) | 155.75 |
| Mitochondrial aconitase 2 (fragment) | Q1P9Q3 | Q1P9Q3_BOVINc | 19 | 21.3 | 20 | 2 | 16 (17) | 424.43 |
| NADH dehydrogenase (ubiquinone) Fe-S protein 7 | Q5RJN0 | Q5RJN0_RAT | 3 | 16.5 | 8 | 2 | 13 (18) | 104.15 |
| NADH-ubiquinone oxidoreductase MLRQ subunit | Q62425 | NDUA4_MOUSE | 3 | 36.6 | 7 | 2 | 13 (16) | 75.72 |
| Prohibitin-2 (B-cell receptor-associated protein BAP37) | Q99623 | PHB2_HUMANc | 5 | 16.7 | 5 | 3 | 17 (20) | 78.89 |
| Ribosomal protein L13a | Q5M9M0 | Q5M9M0_MOUSEc | 18 | 53.7 | 66 | 3 | 17 (15) | 200.01 |
| RRS1 ribosome biogenesis regulator homolog | A1A5P2 | A1A5P2_RAT | 10 | 26.8 | 10 | 3 | 17 (15) | 128.07 |
| Stress-induced-phosphoprotein 1 (STI1) (Hsc70/Hsp90-organizing protein) (Hop) | O35814 | STIP1_RAT | 28 | 46.6 | 28 | 4 | 21 (16) | 227.95 |
| Transcription elongation factor B polypeptide 2 (elongin B) | P62869 | ELOB_MOUSEc | 6 | 39 | 10 | 4 | 22 (14) | 140.23 |
| Ubiquitin-conjugating enzyme E2 variant 2 | A0M8W4 | A0M8W4_HUMANc | 1 | 6.9 | 1 | 5 | 25 (14) | 56.44 |
a
Fraction numbering is indicated as follows: fraction number after the first-dimension separation (corresponding fraction number after the second dimension separation).
b
MS/MS data are indicated for the selected fraction with highest score. See Fig. S1 and S2 in the supplemental material for the full list.
c
The corresponding rat protein can be found in Fig. S3 in the supplemental material.
d
Protein identified by Western blot (WB) analysis of the indicated fraction.