Supporting Information for Proteomics DOI 10.1002/pmic.200500725

Iveta Klouckova, Petra Hrncirova, Yehia Mechref, Randy J. Arnold, Ting-Kai Li, William J. McBride and Milos V. Novotny

Changes in liver protein abundance in inbred alcohol-preferring rats due to chronic alcohol exposure, as measured through a proteomics approach

ª 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com 113 significant proteins GROUP1 GROUP2 ratio of ratio of Coverage average iP1- average iP7- Coverage average iP1- average iP7- Name Abbreviation ssp extract denzity_iP7- ssp extract denzity_iP7- [%] 6" ± "stdev 12" ± "stdev [%] 6" ± "stdev 12" ± "stdev 12/ iP1-6 12/ iP1-6

14-3-3 protein gamma 143G_HUMAN 3209 ex1 24 89 ± 26 53 ± 12 0.59 ± 0.22 2214 ex1 N/A 154 ± 15 136 ± 49 0.89 ± 0.33

Sodium/potassium- transporting ATPase A1A3_RAT 5607 ex1 2 183 ± 119 140 ± 101 0.77 ± 0.75 4727 ex1 2 288 ± 122 100 ± 63 0.35 ± 0.26 alpha-3 chain Aspartate aminotransferase, AATC_RAT 6438 A ex1 8 99 ± 27 67 ± 17 0.67 ± 0.25 6426 ex1 8 348 ± 65 158 ± 61 0.45 ± 0.19 cytoplasmic Acyl-CoA 5328 ex1 14 91 ± 73 48 ± 13 0.53 ± 0.44 5414 ex1 14 486 ± 96 286 ± 99 0.59 ± 0.24 dehydrogenase, ACDB_RAT 7210 ex1 15 181 ± 62 126 ± 32 0.70 ± 0.3 7303 ex1 15 605 ± 125 452 ± 69 0.75 ± 0.19 short/branched chain 5337 B ex1 19 117 ± 60 90 ± 18 0.77 ± 0.43 5429 ex1 19 531 ± 83 273 ± 71 0.52 ± 0.16 Acyl-CoA dehydrogenase, long- ACDL_RAT 5421 C ex1 9 669 ± 151 474 ± 118 0.71 ± 0.24 5417 ex1 N/A 903 ± 267 963 ± 160 1.07 ± 0.36 chain specific Acyl-CoA dehydrogenase, ACDM_RAT 7413 D ex1 19 762 ± 129 606 ± 158 0.80 ± 0.25 7406 ex1 19 1,598 ± 278 1,113 ± 323 0.70 ± 0.24 medium-chain specific Acyl-CoA 6312 E ex1 8 166 ± 45 91 ± 64 0.55 ± 0.41 6407 ex1 8 232 ± 38 176 ± 32 0.76 ± 0.18 dehydrogenase, short - ACDS_RAT 5337 B ex1 9 117 ± 60 90 ± 18 0.77 ± 0.43 5429 ex1 9 531 ± 83 273 ± 71 0.52 ± 0.16 chain specific 5332 F ex3 N/A 154 ± 44 179 ± 88 1.17 ± 0.66 6330 ex3 9 137 ± 36 88 ± 33 0.65 ± 0.29 2441 G ex1 7 86 ± 17 43 ± 13 0.50 ± 0.18 2537 ex1 0 168 ± 20 97 ± 43 0.58 ± 0.27 3343 H ex1 4 187 ± 44 125 ± 18 0.67 ± 0.18 3430 ex1 N/A 298 ± 65 270 ± 50 0.91 ± 0.26 Actin aortic, smooth ACTA_HUMAN 3304 I ex1 N/A 362 ± 265 313 ± 292 0.87 ± 1.03 2315 ex1 10 172 ± 25 127 ± 35 0.74 ± 0.23 muscle 3340 J ex1 4 68 ± 52 32 ± 80 0.46 ± 0.37 3328 ex1 4 153 ± 33 107 ± 18 0.70 ± 0.19 4509 ex2 N/A 362 ± 265 313 ± 292 0.87 ± 1.03 3426 ex2 7 1,105 ± 199 600 ± 271 0.54 ± 0.26 Actin, cytoplasmic 2 ACTG_HUMAN 3515 K ex1 N/A 106 ± 33 116 ± 20 1.09 ± 0.39 3501 ex1 12 164 ± 26 226 ± 62 1.37 ± 0.44 (Gamma-actin) Alcohol 7311 ex1 2 349 ± 74 255 ± 43 0.73 ± 0.2 7405 ex1 2 903 ± 124 676 ± 232 0.75 ± 0.28 ADHA_RAT dehydrogenase A 6238 L ex1 N/A 950 ± 242 866 ± 189 0.91 ± 0.31 6335 ex1 5 2,577 ± 379 2,043 ± 286 0.79 ± 0.16 Alcohol AKA1_RAT 6320 M ex1 N/A 572 ± 201 503 ± 226 0.88 ± 0.5 6333 ex1 19 720 ± 266 389 ± 136 0.54 ± 0.27 dehydrogenase 3-oxo-5-beta-steroid 4- 5325 ex1 23 205 ± 83 71 ± 45 0.35 ± 0.26 too weak ex1 AKD1_RAT dehydrogenase 5333 N ex1 32 1,110 ± 366 748 ± 190 0.67 ± 0.28 5323 ex1 39 2,515 ± 478 1,642 ± 401 0.65 ± 0.2 Fructose- 7329 ex1 4 212 ± 62 123 ± 56 0.58 ± 0.31 7330 ex1 3 424 ± 146 186 ± 151 0.44 ± 0.39 bisphosphate aldolase ALFB_RAT 7303 O ex1 17 246 ± 79 124 ± 40 0.51 ± 0.23 6109 ex2 0 206 ± 90 138 ± 56 0.67 ± 0.4 B 8229 P ex3 2 42 ± 25 147 ± 84 3.52 ± 2.93 8209 ex3 4 196 ± 91 390 ± 168 1.99 ± 1.26 Alpha-methylacyl-CoA AMAC_RAT 5337 B ex1 20 117 ± 60 90 ± 18 0.77 ± 0.43 5429 ex1 20 531 ± 83 273 ± 71 0.52 ± 0.16 racemase Annexin A3 (Annexin ANX3_RAT 4226 ex3 5 779 ± 285 342 ± 124 0.44 ± 0.23 5220 ex3 N/A 217 ± 97 189 ± 57 0.87 ± 0.47 III) (Lipocortin III) Aflatoxin B1 aldehyde 5315 ex1 10 226 ± 29 174 ± 46 0.77 ± 0.23 5310 ex1 N/A 466 ± 62 429 ± 70 0.92 ± 0.19 AR72_RAT reductase member 2 too weak ex1 4324 ff ex1 4 110 ± 29 33 ± 21 0.30 ± 0.2 6320 M ex1 N/A 572 ± 201 503 ± 226 0.88 ± 0.5 6333 ex1 22 720 ± 266 389 ± 136 0.54 ± 0.27 6325 ex3 15 790 ± 503 581 ± 323 0.74 ± 0.62 7310 ex3 15 549 ± 123 244 ± 115 0.45 ± 0.23 Arginase 1 ARGI_RAT 7418 ex2 N/A 331 ± 204 297 ± 134 0.90 ± 0.69 6347 ex2 31 603 ± 254 307 ± 108 0.51 ± 0.28 5332 F ex3 N/A 154 ± 44 179 ± 88 1.17 ± 0.66 6330 ex3 11 137 ± 36 88 ± 33 0.65 ± 0.29 5353 Q ex3 N/A 186 ± 129 154 ± 101 0.83 ± 0.79 6343 ex3 22 187 ± 46 72 ± 47 0.39 ± 0.27 Argininosuccinate ASSY_RAT 6444 R ex1 18 783 ± 290 469 ± 154 0.60 ± 0.3 6430 ex1 15 1,252 ± 331 895 ± 231 0.71 ± 0.26 synthase ATP synthase alpha 6524 S ex3 3 1,061 ± 284 707 ± 184 0.67 ± 0.25 7413 ex3 N/A 561 ± 166 482 ± 204 0.86 ± 0.44 ATPA_RAT chain, m.p. 6527 T ex3 13 354 ± 120 190 ± 35 0.54 ± 0.21 7418 ex3 N/A 255 ± 150 240 ± 103 0.94 ± 0.68 ATP synthase beta 3527 U ex1 19 503 ± 148 309 ± 79 0.62 ± 0.24 3509 ex1 19 553 ± 199 814 ± 267 1.47 ± 0.72 ATPB_RAT chain, m.p. 3513 V ex2 52 8,069 ± 2,811 4,659 ± 3,058 0.58 ± 0.43 3405 ex2 52 3,347 ± 817 2,247 ± 615 0.67 ± 0.25 D-beta- hydroxybutyrate BDH_RAT 8311 W ex2 6 188 ± 68 360 ± 130 1.91 ± 0.98 8201 ex2 N/A 618 ± 139 615 ± 207 0.99 ± 0.4 dehydrogenase, m.p. 6432 X ex1 6 108 ± 25 56 ± 16 0.52 ± 0.19 6420 ex1 6 210 ± 78 121 ± 53 0.58 ± 0.33 Betaine-homocysteine BHMT_RAT S-methyltransferase 8210 ex1 N/A 583 ± 227 615 ± 129 1.06 ± 0.47 7350 ex1 7 1,798 ± 325 2,542 ± 469 1.41 ± 0.37

Beta- BUP1_RAT 5436 Y ex1 17 1,312 ± 382 777 ± 211 0.59 ± 0.24 5425 ex1 12 2,599 ± 754 1,287 ± 430 0.50 ± 0.22 ureidopropionase 6231 ex1 N/A 448 ± 161 425 ± 241 0.95 ± 0.64 6221 ex1 16 1,316 ± 415 793 ± 207 0.60 ± 0.25 Carbonic anhydrase III CAH3_RAT 7306 ex2 N/A 56 ± 51 55 ± 14 0.99 ± 0.93 6241 ex2 7 65 ± 18 107 ± 30 1.65 ± 0.65 6514 ex1 6 1,685 ± 403 1,188 ± 174 0.71 ± 0.2 6610 ex1 36 2,198 ± 557 1,314 ± 636 0.60 ± 0.33 5529 Z ex3 6 197 ± 64 67 ± 32 0.34 ± 0.2 too weak ex3 Catalase CATA_RAT 5537 ex3 3 195 ± 80 68 ± 35 0.35 ± 0.23 too weak ex3 6506 a ex1 8 605 ± 151 460 ± 86 0.76 ± 0.24 6603 ex1 17 559 ± 164 342 ± 147 0.61 ± 0.32 Cystathionine gamma- 6438 A ex1 7 99 ± 27 67 ± 17 0.67 ± 0.25 6426 ex1 7 348 ± 65 158 ± 61 0.45 ± 0.19 CGL_RAT lyase 7413 D ex1 21 762 ± 129 606 ± 158 0.80 ± 0.25 7406 ex1 21 1,598 ± 278 1,113 ± 323 0.70 ± 0.24 3545 b ex1 21 168 ± 17 124 ± 44 0.74 ± 0.27 3627 ex1 N/A 383 ± 62 332 ± 66 0.87 ± 0.22 61 kDa heat shock 4525 c ex1 N/A 111 ± 49 92 ± 35 0.83 ± 0.48 4606 ex1 2 119 ± 48 58 ± 25 0.49 ± 0.29 CH60_MOUSE protein, m.p. too weak ex2 3538 ex2 12 416 ± 142 169 ± 58 0.41 ± 0.2 4506 ex1 N/A 320 ± 124 307 ± 78 0.96 ± 0.44 3634 ex1 13 320 ± 49 640 ± 109 2.00 ± 0.46 Cytochrome P450 CPDI_RAT 3515 K ex1 N/A 106 ± 33 116 ± 20 1.09 ± 0.39 3501 ex1 7 164 ± 26 226 ± 62 1.37 ± 0.44 2D18 Contrapsin-like protease inhibitor 1 CPI1_RAT 4520 d ex1 N/A 153 ± 75 174 ± 53 1.13 ± 0.65 4501 ex1 21 236 ± 51 152 ± 43 0.65 ± 0.23 precursor Calreticulin precursor CRTC_RAT 2549 ex1 28 745 ± 180 447 ± 117 0.60 ± 0.21 2528 ex1 28 2,114 ± 343 1,425 ± 522 0.67 ± 0.27 (CRP55) 3-hydroxyisobutyrate D3HI_RAT 5209 ex3 5 316 ± 48 150 ± 66 0.48 ± 0.22 5225 ex1 26 1,470 ± 185 961 ± 156 0.65 ± 0.13 dehydrogenase, m.p. 4520 d ex1 N/A 153 ± 75 174 ± 53 1.13 ± 0.65 4501 ex1 3 236 ± 51 152 ± 43 0.65 ± 0.23 5539 ex2 N/A 151 ± 105 163 ± 105 1.08 ± 1.03 4543 ex2 3 236 ± 70 387 ± 92 1.64 ± 0.62 Aldehyde 5512 ex1 23 516 ± 221 268 ± 117 0.52 ± 0.32 5503 ex1 N/A 1,009 ± 279 853 ± 381 0.85 ± 0.44 DHAM_RAT dehydrogenase, m.p. 4406 ex3 30 1,646 ± 278 1,026 ± 243 0.62 ± 0.18 5421 ex3 30 806 ± 205 579 ± 260 0.72 ± 0.37 4421 e ex3 5 478 ± 87 324 ± 121 0.68 ± 0.28 4505 ex1 11 136 ± 63 71 ± 28 0.52 ± 0.32 3442 ex3 4 697 ± 113 483 ± 141 0.69 ± 0.23 5415 ex3 4 210 ± 63 148 ± 74 0.71 ± 0.41 Glutamate 4649 ex1 14 1,857 ± 294 1,412 ± 359 0.76 ± 0.23 4628 ex1 14 1,914 ± 622 1,464 ± 562 0.76 ± 0.38 DHE3_RAT dehydrogenase, m.p. 5437 ex3 10 2,206 ± 881 1,563 ± 844 0.71 ± 0.48 6419 ex3 10 1,367 ± 439 2,450 ± 879 1.79 ± 0.86 6205 f ex1 N/A 73 ± 20 79 ± 14 1.09 ± 0.36 5249 ex1 12 132 ± 33 209 ± 52 1.58 ± 0.56 Dihydropteridine DHPR_RAT 7205 ex1 32 399 ± 115 317 ± 64 0.79 ± 0.28 6241 ex1 32 1,118 ± 88 824 ± 191 0.74 ± 0.18 reductase too weak ex2 6264 ex2 7 146 ± 33 87 ± 12 0.60 ± 0.16 6330 g ex1 28 871 ± 200 586 ± 86 0.67 ± 0.18 6428 ex1 28 1,920 ± 210 1,346 ± 307 0.70 ± 0.18 Sorbitol DHSO_RAT 6334 ex3 4 258 ± 107 144 ± 40 0.56 ± 0.28 7315 ex3 4 157 ± 45 91 ± 48 0.58 ± 0.35 dehydrogenase 5436 Y ex1 8 1,312 ± 382 777 ± 211 0.59 ± 0.24 5425 ex1 0 2,599 ± 754 1,287 ± 430 0.50 ± 0.22 3-alpha - 6301 h ex1 56 724 ± 149 511 ± 124 0.71 ± 0.22 5331 ex1 36 1,419 ± 135 1,120 ± 177 0.79 ± 0.15 hydroxysteroid DIDH_RAT 5337 ex3 10 308 ± 92 151 ± 50 0.49 ± 0.22 6218 ex3 N/A 133 ± 36 127 ± 39 0.96 ± 0.39 dehydrogenase 5247 ex1 5 147 ± 29 109 ± 23 0.74 ± 0.22 5241 ex1 5 249 ± 21 193 ± 41 0.78 ± 0.18 D-dopachrome DOPD_RAT 4136 ex1 10 79 ± 34 175 ± 101 2.22 ± 1.61 4108 ex1 30 329 ± 217 816 ± 384 2.48 ± 2 tautomerase 6205 f ex1 N/A 73 ± 20 79 ± 14 1.09 ± 0.36 5249 ex1 13 132 ± 33 209 ± 52 1.58 ± 0.56 6213 i ex1 N/A 665 ± 129 549 ± 128 0.83 ± 0.25 6208 ex1 12 1,105 ± 87 822 ± 169 0.74 ± 0.16 Enoyl-CoA hydratase ECHM_RAT 5235 j ex1 0 130 ± 37 99 ± 28 0.76 ± 0.3 5224 ex1 22 384 ± 55 606 ± 98 1.58 ± 0.34 6307 k ex2 N/A 142 ± 66 133 ± 35 0.94 ± 0.5 5216 ex2 13 162 ± 53 222 ± 23 1.37 ± 0.47 4431 ex3 9 270 ± 58 186 ± 56 0.69 ± 0.25 5434 ex3 9 131 ± 38 99 ± 44 0.75 ± 0.4 4440 m ex1 4 294 ± 108 209 ± 37 0.71 ± 0.29 4524 ex1 9 888 ± 306 465 ± 286 0.52 ± 0.37 Alpha enolase ENOA_RAT 5533 ex1 20 1,132 ± 419 786 ± 230 0.69 ± 0.33 5518 ex1 20 3,140 ± 620 2,159 ± 719 0.69 ± 0.27 too weak ex2 4548 ex2 11 252 ± 57 116 ± 27 0.46 ± 0.15 Electron transfer 6212 n ex1 28 239 ± 60 174 ± 36 0.73 ± 0.24 6308 ex1 28 362 ± 103 259 ± 49 0.72 ± 0.24 flavoprotein alpha- ETFA_RAT 6238 L ex1 N/A 950 ± 242 866 ± 189 0.91 ± 0.31 6335 ex1 6 2,577 ± 379 2,043 ± 286 0.79 ± 0.16 subunit, m.p. too weak ex3 6212 ex3 16 238 ± 105 90 ± 66 0.38 ± 0.32 4332 ex1 N/A 230 ± 87 215 ± 47 0.93 ± 0.41 4404 ex1 11 512 ± 102 296 ± 106 0.58 ± 0.24 Fructose-1,6- too weak ex1 4324 ff ex1 10 110 ± 29 33 ± 21 0.30 ± 0.2 F16P_RAT bisphosphatase 3253 o ex1 N/A 85 ± 57 79 ± 101 0.93 ± 1.35 3235 ex1 3 137 ± 31 59 ± 19 0.43 ± 0.17 too weak ex2 3340 ex2 3 103 ± 30 63 ± 18 0.61 ± 0.25 6408 p ex1 21 2,274 ± 578 1,509 ± 356 0.66 ± 0.23 5432 ex1 21 4,413 ± 584 2,678 ± 666 0.61 ± 0.17 5433 ex3 2 717 ± 127 351 ± 159 0.49 ± 0.24 6336 ex3 2 260 ± 135 209 ± 124 0.80 ± 0.63 6433 ex2 N/A 179 ± 143 162 ± 91 0.90 ± 0.89 5349 ex2 5 355 ± 87 265 ± 46 0.75 ± 0.22 Fumarylacetoacetase FAAA_RAT 5421 C ex1 12 669 ± 151 474 ± 118 0.71 ± 0.24 5417 ex1 N/A 903 ± 267 963 ± 159 1.07 ± 0.36 5436 Y ex1 19 1,312 ± 382 777 ± 211 0.59 ± 0.24 5425 ex1 0 2,599 ± 754 1,287 ± 430 0.50 ± 0.22 6418 q ex2 7 41 ± 27 103 ± 42 2.52 ± 1.98 5415 ex2 N/A 176 ± 64 162 ± 38 0.92 ± 0.4 Fatty acid-binding FABE_RAT 5126 ex1 54 83 ± 36 100 ± 55 1.20 ± 0.84 5116 ex1 54 81 ± 103 243 ± 97 3.00 ± 4 protein 6412 r ex3 3 3,703 ± 1,568 2,870 ± 1,382 0.78 ± 0.5 7401 ex3 3 2,063 ± 551 3,042 ± 803 1.47 ± 0.55 Fibrinogen beta chain 6524 S ex3 6 1,061 ± 284 707 ± 184 0.67 ± 0.25 7413 ex3 N/A 561 ± 166 482 ± 204 0.86 ± 0.44 FIBB_RAT precursor 5529 Z ex3 4 197 ± 64 67 ± 32 0.34 ± 0.2 too weak ex3 6527 T ex3 7 354 ± 120 190 ± 35 0.54 ± 0.21 7418 ex3 N/A 255 ± 150 240 ± 103 0.94 ± 0.68 Fumarate hydratase, FUMH_RAT 7403 ex1 N/A 433 ± 73 363 ± 68 0.84 ± 0.21 6434 ex1 20 967 ± 74 762 ± 160 0.79 ± 0.18 m.p. Glyceraldehyde 3- 6330 g ex1 13 871 ± 200 586 ± 86 0.67 ± 0.18 6428 ex1 13 1,920 ± 210 1,346 ± 307 0.70 ± 0.18 phosphate G3P_RAT 8201 ex1 8 41 ± 17 65 ± 25 1.59 ± 0.9 8207 ex1 11 102 ± 37 199 ± 99 1.95 ± 1.21 dehydrogenase 6332 ex1 14 482 ± 126 370 ± 84 0.77 ± 0.27 6342 ex1 14 675 ± 74 477 ± 108 0.71 ± 0.18 Guanine nucleotide- binding protein beta GBLP_HUMAN 7321 s ex2 N/A 191 ± 202 200 ± 114 1.05 ± 1.25 7210 ex2 3 382 ± 39 504 ± 110 1.32 ± 0.32 subunit-like protein 12.3 Glycine N- 6212 n ex1 25 239 ± 60 174 ± 36 0.73 ± 0.24 6308 ex1 25 362 ± 103 259 ± 49 0.72 ± 0.24 GLMT_RAT methyltransferase 6238 L ex1 N/A 950 ± 242 866 ± 189 0.91 ± 0.31 6335 ex1 35 2,577 ± 379 2,043 ± 286 0.79 ± 0.16 6408 p ex1 11 2,274 ± 578 1,509 ± 356 0.66 ± 0.23 5432 ex1 11 4,413 ± 584 2,678 ± 666 0.61 ± 0.17 Glutamine synthetase GLNA_RAT 5436 Y ex1 0 1,312 ± 382 777 ± 211 0.59 ± 0.24 5425 ex1 8 2,599 ± 754 1,287 ± 430 0.50 ± 0.22 Stress-70 protein, m.p. GR75_RAT 3545 b ex1 4 168 ± 17 124 ± 44 0.74 ± 0.27 3627 ex1 N/A 383 ± 62 333 ± 66 0.87 ± 0.22 Glutathione GSHB_RAT 3527 U ex1 17 503 ± 148 309 ± 79 0.62 ± 0.24 3509 ex1 17 553 ± 199 814 ± 267 1.47 ± 0.72 synthetase 6111 t ex1 7 414 ± 90 271 ± 63 0.66 ± 0.21 6214 ex1 7 1,107 ± 155 543 ± 164 0.49 ± 0.16 Glutathione S- GTM1_RAT 7118 u ex1 7 1,706 ± 534 1,118 ± 171 0.66 ± 0.23 7209 ex1 7 5,081 ± 815 3,037 ± 582 0.60 ± 0.15 transferase Yb-1 5217 ex1 N/A 229 ± 66 257 ± 89 1.13 ± 0.51 5208 ex1 6 565 ± 93 771 ± 95 1.36 ± 0.28 6111 t ex1 42 414 ± 90 271 ± 63 0.66 ± 0.21 6214 ex1 42 1,107 ± 155 543 ± 164 0.49 ± 0.16 7118 u ex1 57 1,706 ± 534 1,118 ± 171 0.66 ± 0.23 7209 ex1 57 5,081 ± 815 3,037 ± 582 0.60 ± 0.15 7319 ex2 18 66 ± 34 112 ± 46 1.69 ± 1.11 7207 ex2 18 268 ± 68 158 ± 37 0.59 ± 0.2 Glutathione S- 5132 v ex3 12 386 ± 194 107 ± 87 0.28 ± 0.26 too weak ex3 GTM2_RAT transferase Yb-2 7209 ex1 0 70 ± 29 248 ± 347 3.53 ± 5.16 7205 ex1 6 225 ± 52 323 ± 82 1.44 ± 0.49 6112 w ex1 0 159 ± 77 125 ± 29 0.79 ± 0.42 6216 ex1 16 305 ± 38 246 ± 52 0.80 ± 0.2 7107 ex1 6 79 ± 22 53 ± 26 0.67 ± 0.38 6238 ex1 6 346 ± 60 137 ± 50 0.39 ± 0.16 5223 x ex3 6 300 ± 96 222 ± 63 0.74 ± 0.32 6216 ex3 6 305 ± 38 67 ± 22 0.49 ± 0.19 Glutathione S- GTP_RAT 7152 ex1 10 56 ± 24 34 ± 9 0.60 ± 0.3 6239 ex1 25 112 ± 35 70 ± 20 0.62 ± 0.26 transferase p Glutathione S- GTT2_RAT too weak ex1 7227 ex1 9 108 ± 37 42 ± 19 0.39 ± 0.22 transferase YRS-YRS 4421 e ex3 11 478 ± 87 324 ± 121 0.68 ± 0.28 4505 ex1 11 136 ± 63 71 ± 28 0.52 ± 0.32 Guanine deaminase GUAD_RAT 4414 y ex1 N/A 50 ± 46 53 ± 36 1.06 ± 1.21 3540 ex1 6 306 ± 113 143 ± 57 0.47 ± 0.26 Hydroxyacid oxidase 3 HAO3_RAT 7313 ex1 0 95 ± 22 75 ± 7 0.79 ± 0.2 7409 ex1 3 173 ± 35 107 ± 53 0.62 ± 0.33 Short chain 3- 8202 ex1 N/A 681 ± 298 723 ± 143 1.06 ± 0.51 7350 ex1 22 1,798 ± 325 2,542 ± 469 1.41 ± 0.37 HCDH_RAT hydroxyacyl-CoA 8229 P ex3 0 42 ± 25 147 ± 84 3.52 ± 2.93 8209 ex3 15 196 ± 91 390 ± 168 1.99 ± 1.26 Delta-aminolevulinic HEM2_RAT too weak ex1 4326 ex1 11 181 ± 48 107 ± 21 0.59 ± 0.19 acid dehydratase Haptoglobin precursor HPT_RAT 4414 y ex1 N/A 49 ± 47 54 ± 34 1.11 ± 1.27 3540 ex1 4 306 ± 113 143 ± 57 0.47 ± 0.26 Heat shock cognate 3526 ex3 2 335 ± 97 175 ± 66 0.52 ± 0.25 4547 ex3 2 334 ± 192 249 ± 76 0.75 ± 0.49 HS7C_MOUSE 71 kDa protein 3530 ex3 2 595 ± 216 307 ± 106 0.52 ± 0.26 3641 ex1 17 310 ± 102 119 ± 28 0.38 ± 0.16 Heat shock protein HS9B_RAT 5604 ex1 2 134 ± 90 84 ± 34 0.63 ± 0.49 4724 ex1 2 159 ± 63 49 ± 34 0.31 ± 0.24 HSP 90-beta Isocitrate 6408 p ex1 34 2,274 ± 578 1,509 ± 356 0.66 ± 0.23 5432 ex1 34 4,413 ± 584 2,678 ± 666 0.61 ± 0.17 IDHC_RAT dehydrogenase 5417 ex3 3 408 ± 101 197 ± 101 0.48 ± 0.28 6323 ex3 3 281 ± 95 585 ± 338 2.08 ± 1.39 Adenylate kinase 5249 ex1 5 190 ± 36 142 ± 28 0.75 ± 0.21 5240 ex1 5 421 ± 57 335 ± 69 0.80 ± 0.2 isoenzyme 2, KAD2_RAT 5223 x ex3 10 300 ± 96 222 ± 63 0.74 ± 0.32 6216 ex3 10 305 ± 38 67 ± 22 0.49 ± 0.19 mitochondrial 7209 ex1 10 70 ± 29 248 ± 347 3.53 ± 5.16 7205 ex1 14 225 ± 52 323 ± 82 1.44 ± 0.49 Adenylate kinase isoenzyme 4, KAD4_RAT 7322 ex2 13 89 ± 88 116 ± 53 1.30 ± 1.42 7212 ex2 13 171 ± 43 272 ± 57 1.59 ± 0.52 mitochondrial cAMP-dependent 6444 R ex1 4 783 ± 290 469 ± 154 0.60 ± 0.3 6430 ex1 0 1,252 ± 331 895 ± 231 0.71 ± 0.26 protein kinase, alpha- KAPA_RAT too weak ex2 4323 ex2 4 140 ± 36 71 ± 34 0.50 ± 0.28 catalytic subunit 4332 ex3 4 272 ± 115 128 ± 76 0.47 ± 0.34 5326 ex3 4 149 ± 52 86 ± 37 0.58 ± 0.32 Acyl-protein LYA1_RAT 5101 ex1 N/A 241 ± 51 234 ± 36 0.97 ± 0.25 4227 ex1 8 615 ± 95 789 ± 92 1.28 ± 0.25 thioesterase 1 S-adenosylmethionine 3340 J ex1 6 68 ± 52 32 ± 8 0.46 ± 0.37 3328 ex1 6 153 ± 33 107 ± 18 0.70 ± 0.19 METL_RAT synthetase alpha and 4440 m ex1 4 294 ± 108 209 ± 37 0.71 ± 0.29 4524 ex1 25 888 ± 306 465 ± 286 0.52 ± 0.37 Methylmalonate- 6412 r ex3 6 3,703 ± 1,568 2,870 ± 1,382 0.78 ± 0.5 7401 ex3 6 2,063 ± 551 3,042 ± 803 1.47 ± 0.55 semialdehyde MMSA_RAT 6524 S ex3 4 1,061 ± 284 707 ± 184 0.67 ± 0.25 7413 ex3 N/A 561 ± 166 482 ± 204 0.86 ± 0.44 dehydrogenase 6527 T ex3 10 354 ± 120 190 ± 35 0.54 ± 0.21 7418 ex3 N/A 255 ± 150 240 ± 103 0.94 ± 0.68 Myelin proteolipid MYPR_RAT too weak ex2 4229 ex2 3 65 ± 27 98 ± 23 1.52 ± 0.72 protein Nucleoside NDKA_RAT 5205 ex2 10 343 ± 204 94 ± 121 0.28 ± 0.39 too weak ex2 diphosphate kinase A Nucleoside NDKB_RAT 6114 ex1 N/A 322 ± 123 275 ± 37 0.85 ± 0.35 6107 ex1 19 808 ± 91 549 ± 164 0.68 ± 0.22 diphosphate kinase B Nonspecific lipid- NLTP_RAT 6506 a ex1 0 605 ± 151 460 ± 86 0.76 ± 0.24 6603 ex1 4 559 ± 164 342 ± 147 0.61 ± 0.32 transfer protein 2-oxoisovalerate dehydrogenase alpha ODBA_RAT 4439 z ex1 0 169 ± 68 307 ± 336 1.82 ± 2.13 4419 ex1 3 223 ± 71 405 ± 129 1.82 ± 0.82 subunit Pyruvate dehydrogenase E1 ODPB_RAT too weak ex2 3237 ex2 4 58 ± 29 110 ± 36 1.89 ± 1.12 component beta subunit Ornithine 5333 N ex1 0 1,127 ± 370 748 ± 190 0.66 ± 0.28 5323 ex1 7 2,515 ± 478 1,642 ± 401 0.65 ± 0.2 OTC_RAT carbamoyltransferase, 5353 Q ex3 N/A 186 ± 129 154 ± 101 0.83 ± 0.79 6343 ex3 9 187 ± 46 72 ± 47 0.39 ± 0.27 Propionyl-CoA carboxylase alpha PCCA_RAT 4520 ex3 12 132 ± 62 48 ± 42 0.37 ± 0.36 too weak ex3 chain, m.p. 3546 ex3 2 332 ± 45 180 ± 93 0.54 ± 0.29 5409 ex3 2 173 ± 88 76 ± 32 0.44 ± 0.29 4525 c ex1 N/A 111 ± 49 92 ± 35 0.83 ± 0.48 4606 ex1 5 119 ± 48 58 ± 25 0.49 ± 0.29 Protein disulfide too weak ex2 3538 ex2 28 416 ± 142 169 ± 58 0.41 ± 0.2 isomerase A3 PDA3_RAT 4515 ex3 2 248 ± 92 94 ± 44 0.38 ± 0.23 5424 ex3 2 191 ± 99 136 ± 74 0.71 ± 0.54 precursor 6506 a ex1 0 605 ± 151 460 ± 86 0.76 ± 0.24 6603 ex1 2 559 ± 164 342 ± 147 0.61 ± 0.32 4526 ex2 5 202 ± 165 76 ± 50 0.37 ± 0.39 3537 ex2 5 106 ± 41 200 ± 62 1.89 ± 0.93 Protein disulfide 3513 V ex2 14 8,069 ± 2,811 4,659 ± 3,058 0.58 ± 0.43 3405 ex2 14 3,347 ± 817 2,247 ± 615 0.67 ± 0.25 PDA6_RAT isomerase A6 4507 aa ex2 N/A 121 ± 113 120 ± 97 0.99 ± 1.23 3416 ex2 3 640 ± 130 363 ± 145 0.57 ± 0.25 Protein disulfide PDI_RAT 3520 bb ex1 32 1,394 ± 219 1,083 ± 262 0.78 ± 0.22 3502 ex1 32 2,863 ± 904 2,007 ± 306 0.70 ± 0.25 isomerase precursor 6108 ex1 4 443 ± 155 261 ± 87 0.59 ± 0.28 6210 ex1 52 592 ± 207 228 ± 77 0.39 ± 0.19 7122 ex1 51 773 ± 143 531 ± 128 0.69 ± 0.21 7104 ex1 51 1,641 ± 317 1,155 ± 303 0.70 ± 0.23 Peroxiredoxin 1 PDX1_RAT too weak ex3 7118 ex3 20 449 ± 235 194 ± 43 0.43 ± 0.25 5202 ex1 10 97 ± 32 77 ± 20 0.79 ± 0.33 4222 ex1 10 268 ± 68 182 ± 53 0.68 ± 0.26 Phosphatidylethanola PEBP_RAT 4108 ex1 N/A 319 ± 123 362 ± 121 1.14 ± 0.58 3124 ex1 30 826 ± 389 1,370 ± 199 1.66 ± 0.82 mine-binding protein Phenylalanine-4- PH4H_RAT 4435 ex1 4 219 ± 48 174 ± 45 0.79 ± 0.27 4520 ex1 4 435 ± 139 188 ± 57 0.43 ± 0.19 hydroxylase Prohibitin PHB_MOUSE 4315 cc ex2 N/A 1,331 ± 708 1,095 ± 359 0.82 ± 0.51 3244 ex2 42 1,086 ± 62 1,618 ± 232 1.49 ± 0.23 Phosphoglycerate PMG1_RAT 6213 i ex1 N/A 665 ± 129 549 ± 128 0.83 ± 0.25 6208 ex1 18 1,105 ± 87 822 ± 169 0.74 ± 0.16 mutase 1 Voltage-dependent 8311 W ex2 12 188 ± 68 360 ± 130 1.91 ± 0.98 8201 ex2 N/A 618 ± 139 615 ± 207 1.00 ± 0.4 anion-selective POR1_RAT 7321 s ex2 N/A 191 ± 202 200 ± 114 1.05 ± 1.25 7210 ex2 4 382 ± 39 504 ± 110 1.32 ± 0.32 channel protein 1 8229 P ex3 5 42 ± 25 147 ± 84 3.52 ± 2.93 8209 ex3 10 196 ± 91 390 ± 168 1.99 ± 1.26 Lysosomal acid phosphatase PPAL_RAT 5425 ex3 2 1,032 ± 431 726 ± 398 0.70 ± 0.48 6411 ex3 2 828 ± 349 1,527 ± 566 1.84 ± 1.04 precursor 26S protease PRS7_RAT 4439 z ex1 0 169 ± 68 307 ± 336 1.82 ± 2.13 4419 ex1 9 223 ± 71 405 ± 129 1.82 ± 0.82 regulatory subunit 7 26S protease PRSA_RAT 4507 aa ex2 N/A 121 ± 113 120 ± 97 0.99 ± 1.23 3416 ex2 6 640 ± 130 363 ± 145 0.57 ± 0.25 regulatory subunit 6A Proteasome subunit PSA2_RAT 6112 w ex1 4 159 ± 77 125 ± 29 0.79 ± 0.42 6216 ex1 17 305 ± 38 246 ± 52 0.80 ± 0.2 alpha type 2 Proteasome subunit PSB2_RAT 6116 ex1 5 248 ± 154 195 ± 53 0.79 ± 0.53 6109 ex1 5 505 ± 95 377 ± 81 0.75 ± 0.21 beta type 2 Proteasome subunit PSB3_RAT 5218 ex1 0 49 ± 30 31 ± 21 0.63 ± 0.58 5208 ex1 11 565 ± 93 771 ± 95 1.36 ± 0.28 beta type 3 GTP-binding nuclear RAN_HUMAN 6118 ex1 N/A 59 ± 28 55 ± 18 0.94 ± 0.54 6225 ex1 5 152 ± 48 77 ± 25 0.51 ± 0.23 protein RAN Ribonuclease inhibitor RINI_RAT 2441 G ex1 9 86 ± 17 43 ± 13 0.50 ± 0.18 2537 ex1 3 168 ± 20 97 ± 43 0.58 ± 0.27 60S acidic ribosomal RLA0_RAT 5309 ex3 3 236 ± 96 117 ± 55 0.49 ± 0.31 too weak ex3 protein P0 40S ribosomal protein RS12_MOUSE 6207 ex2 14 82 ± 32 167 ± 47 2.04 ± 0.98 5112 ex2 14 171 ± 69 278 ± 54 1.63 ± 0.73 S12 40S ribosomal protein RSSA_RAT 4315 cc ex2 N/A 1,331 ± 708 1,095 ± 359 0.82 ± 0.51 3244 ex2 6 1,086 ± 62 1,618 ± 232 1.49 ± 0.23 SA SEC14-like protein 2 S142_RAT 6432 X ex1 10 108 ± 25 56 ± 16 0.52 ± 0.19 6420 ex1 10 210 ± 78 121 ± 53 0.58 ± 0.33 3337 ex1 18 233 ± 91 134 ± 32 0.57 ± 0.26 3324 ex1 18 219 ± 40 162 ± 28 0.74 ± 0.18 3347 ex1 56 1,798 ± 344 1,269 ± 277 0.71 ± 0.21 3332 ex1 N/A 2,623 ± 239 2,354 ± 398 0.90 ± 0.17 Senescence marker 3217 ex1 24 230 ± 138 110 ± 28 0.48 ± 0.31 3208 ex1 8 414 ± 90 187 ± 32 0.45 ± 0.13 SM30 RAT SM30_RAT protein-30 4235 ex1 N/A 51 ± 43 45 ± 31 0.88 ± 0.96 4207 ex1 16 108 ± 29 73 ± 18 0.67 ± 0.24 3241 ex1 6 331 ± 182 169 ± 59 0.51 ± 0.33 3223 ex1 6 649 ± 80 420 ± 69 0.65 ± 0.13 3253 o ex1 N/A 84 ± 57 79 ± 101 0.93 ± 1.36 3235 ex1 18 137 ± 31 59 ± 19 0.43 ± 0.17 Superoxide dismutase SODM_RAT 7132 ex1 N/A 235 ± 62 234 ± 42 1.00 ± 0.32 7111 ex1 14 564 ± 81 829 ± 196 1.47 ± 0.41 [Mn], m.p. DOPA/tyrosine SU1B_RAT 7227 ex1 N/A 169 ± 47 140 ± 59 0.83 ± 0.42 7319 ex1 4 591 ± 103 438 ± 86 0.74 ± 0.19 sulfotransferase N-hydroxyarylamine 5311 ex1 23 1,179 ± 442 690 ± 159 0.59 ± 0.26 5303 ex1 23 2,258 ± 483 1,761 ± 403 0.78 ± 0.24 SUAC_RAT sulfotransferase 4349 ex1 12 138 ± 32 106 ± 22 0.77 ± 0.24 4327 ex1 12 251 ± 58 138 ± 44 0.55 ± 0.22 Aryl sulfotransferase SUAR_RAT 6301 h ex1 0 724 ± 149 511 ± 124 0.71 ± 0.22 5331 ex1n 8 1,419 ± 135 1,120 ± 177 0.79 ± 0.15 5518 ex1 N/A 1,139 ± 329 1,055 ± 292 0.93 ± 0.37 5615 ex1 4 2,389 ± 462 1,584 ± 288 0.66 ± 0.18 3313 ex1 4 88 ± 66 16 ± 16 0.18 ± 0.23 too weak ex1 Tubulin alpha-1 chain TBA1_MOUSE 3520 bb ex1 4 1,394 ± 219 1,083 ± 262 0.78 ± 0.22 3502 ex1 4 2,863 ± 904 2,007 ± 306 0.70 ± 0.25 3343 H ex1 4 187 ± 44 125 ± 18 0.67 ± 0.18 3430 ex1 N/A 298 ± 65 270 ± 49 0.91 ± 0.26 Transitional endoplasmic reticulum TERA_RAT 3540 ex1 2 105 ± 58 66 ± 16 0.63 ± 0.38 3622 ex1 2 153 ± 25 93 ± 31 0.61 ± 0.23 ATPase 3-ketoacyl-CoA thiolase B, THIK_RAT 6312 E ex1 5 166 ± 45 91 ± 64 0.55 ± 0.41 6407 ex1 5 232 ± 38 176 ± 32 0.76 ± 0.18 peroxisomal precursor 6438 A ex1 3 99 ± 27 67 ± 17 0.67 ± 0.25 6426 ex1 3 348 ± 65 158 ± 61 0.45 ± 0.19 3-ketoacyl-CoA 6432 X ex1 7 108 ± 25 56 ± 16 0.52 ± 0.19 6420 ex1 7 210 ± 78 121 ± 53 0.58 ± 0.33 THIM_RAT thiolase 6418 q ex2 9 41 ± 27 103 ± 42 2.52 ± 1.98 5415 ex2 N/A 176 ± 64 162 ± 38 0.92 ± 0.4 7413 D ex1 16 762 ± 129 606 ± 158 0.80 ± 0.25 7406 ex1 16 1,598 ± 278 1,113 ± 323 0.70 ± 0.24 7303 O ex1 31 246 ± 79 124 ± 40 0.51 ± 0.23 6109 ex2 0 206 ± 90 138 ± 56 0.67 ± 0.4 too weak ex1 7327 ex1 11 545 ± 250 274 ± 133 0.50 ± 0.34 Thiosulfate THTR_RAT 3304 I ex1 N/A 362 ± 265 313 ± 292 0.87 ± 1.03 2315 ex1 6 172 ± 25 127 ± 35 0.74 ± 0.23 sulfurtransferase 7238 dd ex3 N/A 5,189 ± 4,970 5,053 ± 4,716 0.97 ± 1.3 7242 ex3 6 1,735 ± 1,144 3,559 ± 1,566 2.05 ± 1.63 7341 ee ex3 N/A 116 ± 90 129 ± 41 1.11 ± 0.93 7248 ex3 21 176 ± 78 384 ± 163 2.18 ± 1.34 Transketolase TKT_RAT too weakex1 6633 ex1 20 125 ± 64 40 ± 21 0.32 ± 0.24 5132 v ex3 12 386 ± 194 107 ± 87 0.28 ± 0.26 too weak ex3 Triosephosphate TPIS_RAT 5235 j ex1 27 130 ± 37 99 ± 28 0.76 ± 0.3 5224 ex1 5 384 ± 55 606 ± 98 1.58 ± 0.34 isomerase 6307 k ex2 N/A 142 ± 66 133 ± 35 0.94 ± 0.5 5216 ex2 6 162 ± 53 222 ± 23 1.37 ± 0.47 Serotransferin TRFE_RAT 6628 ex1 2 157 ± 107 117 ± 26 0.74 ± 0.53 6724 ex1 2 207 ± 46 133 ± 64 0.64 ± 0.34 precursor 14.5 kDa translational UK14_RAT 7207 ex2 40 570 ± 371 350 ± 99 0.61 ± 0.44 6126 ex2 40 743 ± 189 525 ± 96 0.71 ± 0.22 inhibitor protein 7313 ex2 N/A 45 ± 55 51 ± 50 1.12 ± 1.77 7302 ex2 13 207 ± 47 131 ± 45 0.63 ± 0.26 Uricase URIC_RAT 7238 dd ex3 N/A 5,189 ± 4,970 5,053 ± 4,716 0.97 ± 1.3 7242 ex3 10 1,735 ± 1,144 3,559 ± 1,566 2.05 ± 1.63 7341 ee ex3 N/A 116 ± 90 129 ± 41 1.11 ± 0.93 7248 ex3 35 176 ± 78 384 ± 163 2.18 ± 1.34 Notes: m.p. = mitochondrial precursor N/A = spot was not identified by LC-MS/MS in this group Coverage [%] = 0, protein was not identified in the spot from this group, but was identified in the same spot in other group. Italics indicates spot intensities are not statistically signficant in this group; spots are assignment by position on the gel. Bold font indicates the spot displayed one of the five largest up- or down-regulations for that group.