TABLE 1.
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 |
Fraction numbering is indicated as follows: fraction number after the first-dimension separation (corresponding fraction number after the second dimension separation).
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.
The corresponding rat protein can be found in Fig. S3 in the supplemental material.
Protein identified by Western blot (WB) analysis of the indicated fraction.