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.