Supporting Information for Proteomics DOI 10.1002/pmic.200600983 Julia Strathmann, Krisztina Paal, Carina Ittrich, Eberhard Krause, Klaus E. Appel, Howard P. Glauert, Albrecht Buchmann and Michael Schwarz Proteome analysis of chemically induced mouse liver tumors with different genotype ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com A. 2DE pictures Normal liver GS negative GS positive MW pI 3 10 B. Zoomed regions 1. Expression of GS 2. Expression of GST M2 3. A. Expression of MUP 8/11 3. B. Expression of MUP 2 4. Expression of Annexin A2 5. Expression of regucalcin: identified in 3 different spots % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 650.0393 672.0223 666.0108 Acetyl 707.2025 776.1843 842.5089 877.0358 905.6765 967.9841 1066.0697 1150.0699 1143.0863 1281.6 - 1224.1243 CoA acetyltransferase 1307.7966 1335.1716 1404.7513 1531.8387 1621.8403 1684.9310 4700 ReflectorSpec#1[BP=1753.9,424] 1753.9518 1796.9624 1964.2 1875.0048 Q8CAY6 1938.9302 1934.9824 1964.9377 2043.1290 Mass (m/z) 2142.0527 2211.1064 2233.1333 2226.1382 2292.2849 2284.1768 2322.2368 2338.2627 2384.2915 2453.2107 2447.2783 2646.8 2576.3389 2654.2969 2667.3318 2745.3074 2866.4612 , cytosolic 3329.4 3244.7070 , 4012.0 424.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 628.0881 644.0302 666.0172 701.4904 815.4185 842.5089 881.2626 877.0427 870.5422 976.4503 Actin Cytoplasmic 1045.5627 1066.0701 1106.5577 1132.5288 1281.6 1198.7013 1361.8008 1516.7139 P60710, Score152 1629.8191 1688.8756 4700 ReflectorSpec#1[BP=842.5,689] 1794.8589 1790.8900 1964.2 1853.8925 1954.0649 1986.0228 Mass (m/z) 2226.1201 2211.1040 2285.1621 2382.1338 1( 2646.8 2539.1863 beta actin 3329.4 ), 4012.0 688.8 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 656.0695 679.5138 795.4752 856.5247 842.5089 945.5387 Actin Cytoplasmic 976.4440 1045.5591 1106.5510 1132.5244 1164.7384 1281.6 1198.6996 1231.6733 1354.6144 1461.7360 1516.7034 P60710, Score400 1547.7396 1629.8165 4700 ReflectorSpec#1[BP=1198.7,1496] 1746.8453 1790.8829 1838.7776 1964.2 1954.0613 1976.0229 2084.0659 Mass (m/z) 2216.0757 2211.1038 2284.1619 2343.1553 1( 2475.1460 2646.8 2550.1672 beta actin 2750.2891 3137.5925 3199.6357 3329.4 3338.7297 ), 4012.0 1496.5 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 644.3745 758.8766 842.5090 976.4437 Actin Cytoplasmic 1045.5402 1111.6035 1132.5186 1281.8 1171.5673 1198.6964 1236.5779 1354.6180 1499.6642 1516.7151 P60710, Score470 1592.8094 4700 ReflectorSpec#1[BP=1790.9,2808] 1746.8669 1790.8763 1822.7810 1964.6 1915.9297 1960.8990 1954.0522 1993.9595 Mass (m/z) 2211.1038 2215.0554 2284.1641 2343.1519 1( 2647.4 2550.1470 beta actin 2730.3281 2807.3477 3183.5964 3330.2 3251.4219 3338.7551 3413.6157 ), 3491.6208 3555.6621 4013.0 2808.2 Actin Cytoplasmic 1 (beta actin), P60710, Score 393 4700 Reflector Spec #1[BP = 1790.9, 921] 100 1790.8904 921.0 90 80 70 1198.7015 60 50 % Intensity 40 1954.0656 30 20 842.5090 2211.1062 1132.5289 10 1516.7206 666.0146 978.0363 1629.8209 2285.1748 2550.1917 893.0243 1977.0419 1036.6520 795.4677 1812.8555 1221.7039 3199.6316 1744.8641 2384.0688 1315.5662 0 599.0 1281.6 1964.2 2646.8 3329.4 4012.0 Mass (m/z) % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 679.5235 795.4698 842.5089 870.5468 4- 976.4493 mitochondrial precursor 1045.5627 1106.5598 aminobutyrate aminotransferase 1132.5289 1281.8 1187.5555 1198.7042 1231.6796 1282.5927 1354.6279 1475.7566 1461.7422 1516.7252 1547.7468 1623.8331 4700 ReflectorSpec#1[BP=1790.9,1042] 1707.8058 1790.8885 1822.8090 1964.6 1954.0664 1976.9465 2099.0430 Mass (m/z) 2225.1252 2211.1035 2284.1775 2359.1765 2647.4 2567.2017 2628.2463 2870.4541 , P61922 3138.5989 3199.6423 3330.2 3723.9290 4013.0 1041.5 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 679.5110 662.3986 795.4604 842.5090 856.5297 870.5416 Alpha-1- 963.5132 1045.5637 1070.5369 1108.5952 1104.6084 1281.6 1179.5991 1257.6239 1320.5909 1420.7356 1516.7264 1585.7773 antitrypsin 1652.7773 4700 ReflectorSpec#1[BP=1070.5,3904] 1730.9104 1790.8865 1964.2 1851.9172 1940.9385 Q00897 2000.0323 2003.9980 2041.9832 2083.0164 Mass (m/z) 2221.1211 2211.1042 2284.1719 2367.0718 2432.2224 1-4 2646.8 2549.1531 2634.3521 2705.1321 2808.2993 precursor 2914.5293 3028.6248 3090.6089 3329.4 3252.7480 3347.6755 3499.7815 , 3742.4299 4012.0 3904.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 650.0491 666.0205 727.4628 815.5123 877.0413 948.5746 1035.5275 1111.5500 1281.6 1277.7108 1343.8066 1432.6624 1421.6912 Annexin 1470.2003 1491.8658 1560.7603 1542.8427 1628.9364 1650.9790 4700 ReflectorSpec#1[BP=1542.8,4467] 1688.9087 1747.9241 1779.8154 1848.9506 1964.2 1908.8827 1993.9749 2105.0137 A2,P07356 Mass (m/z) 2211.1042 2288.1689 2284.1729 2367.2612 2480.2307 2646.8 2664.3662 2780.9927 2838.4138 2923.3550 2938.3787 2999.3989 3095.6091 3329.4 3339.7539 3635.9451 4012.0 4467.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 660.0098 650.0457 681.9913 666.0161 727.4576 787.4554 881.2709871.0233 Fumarate hydratase 971.2996 1031.5612 1116.60791106.5530 1281.6 1234.6249 1332.6622 1426.8475 1442.8418 1498.8510 1560.7795 precursor 1644.8098 4700 ReflectorSpec#1[BP=1763.9,1423] 1724.8716 1763.9237 1794.7975 1964.2 1853.9353 1927.0150 1988.0818 2070.0591 Mass (m/z) 2141.0850 2225.1213 2211.1040 2284.1694 , P97807 2307.1650 2300.1794 2376.1792 2467.2119 , 2483.2375 mitochondrial 2646.8 2557.2766 2663.3074 2781.4595 2914.5171 3121.5525 3182.5649 3329.4 3286.5994 3347.5845 3496.7319 4012.0 1423.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 628.0757 644.0302 666.0161 695.1690 679.5115 771.4939 849.0469 833.0671 871.0224855.0512 907.2377917.2798 996.6064 1082.0454 1106.5570 1150.5891 1281.6 1271.0764 1364.6718 Annexin 1458.7570 1528.7466 1623.7616 4700 ReflectorSpec#1[BP=2212.1,2565] 1704.8688 1794.8191 1964.2 1873.9042 1868.8792 1940.9457 2025.9644 A3,O35639 Mass (m/z) 2137.0820 2211.1040 2239.1331 2225.1233 2284.1772 2314.1941 2300.1794 2402.2681 2480.2939 2646.8 2541.2512 2663.3640 2721.2578 2781.4697 2914.4990 3096.6270 3329.4 3338.7268 4012.0 2564.7 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 666.0195 688.0060 774.8920 842.5090 900.4556 975.4771 1001.5952 1014.5106 1076.0389 1106.5778 1155.5638 1281.6 1234.6713 1268.5865 1290.6289 1432.7452 Annexin 1531.7677 1548.7688 1659.8832 4700 ReflectorSpec#1[BP=1799.9,1055] 1703.8787 1749.8678 1799.8915 1821.8617 1836.9589 1964.2 1942.8949 2005.5322 2022.9894 2109.1582 A5,P48036 Mass (m/z) 2151.0847 2211.1038 2284.1436 2646.8 2915.2512 3329.4 3883.7710 4012.0 1055.4 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 666.0172 Arginase 757.3782 893.0151 948.5461 1010.0403 1082.0381 arginase 1152.5870 1161.6438 1281.6 1285.6378 1357.6819 -1 (TypeI 1456.7607 1460.7017 1444.7058 1635.8414 4700 ReflectorSpec#1[BP=1910.0,3137] 1693.7960 1764.4441 , Q61176,Score588 1822.9733 1964.2 1857.9951 1896.9578 1909.9738 1969.9567 2018.0718 2042.5602 2093.0479 Mass (m/z) 2130.9941 2203.0708 2225.0974 arginase 2284.1897 2502.2231 2646.8 2567.2808 2706.1631 2782.4546 ) livertype 3113.5737 3329.4 3269.7227 3339.7168 3397.8086 3525.8887 4012.0 3136.9 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 628.0848 644.0328 666.0200 697.9635 681.9938 771.4896 842.5089 877.0427 902.9794 948.5489 1009.5405 Arginase 1082.0433 1157.5959 1143.0886 1281.6 1332.6711 1398.6594 1444.7135 1509.6848 1603.8058 1670.8756 4700 ReflectorSpec#1[BP=1911.0,1619] 1693.8060 -1, Q61176,Score158 1812.9609 1964.2 1857.9966 1873.9972 1914.9839 1909.9738 2003.0503 2018.0724 2093.0532 Mass (m/z) 2158.0608 2211.1038 2240.13602225.1221 2284.1716 2314.1970 2299.1892 2403.2839 2463.2268 2646.8 2663.3516 2722.2380 2780.9580 2914.4883 3096.6008 3329.4 3269.7510 3338.7449 3812.6619 4012.0 1618.7 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 639.4114 666.0236 743.4389 831.4809 893.0197 989.5396 1004.5209 Argininsuccinate lyase 1088.5040 1157.5931 1281.6 1253.6364 1265.6147 1315.6487 1373.7021 1445.7462 1481.7059 1549.7283 1620.8109 4700 ReflectorSpec#1[BP=1934.1,1012] 1692.8912 1676.8923 1776.8433 1964.2 1851.9309 1916.0519 1933.0768 2002.0015 2023.0021 2040.0249 2089.1655 Mass (m/z) 2211.1030 2322.0920 2401.2759 2466.1870 2646.8 2534.3523 2622.2751 2705.1702 2780.3923 , Q91YI0 2875.3098 3329.4 3338.7627 3771.9731 4012.0 1012.0 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 672.0247 666.0132 ATP 779.4278 842.5090 877.0328 960.0540 1045.5618 synthasebetachain 1106.5563 1088.6304 1281.6 1168.0807 1262.6412 1314.6086 1391.6755 1401.7020 1406.6768 1435.7455 1475.8306 1555.7953 precursor 1601.8090 1633.8062 1617.8019 4700 ReflectorSpec#1[BP=1989.0,1097] 1762.9443 1780.9612 1842.8795 1964.2 1874.8694 1858.8761 1919.0919 1942.0385 1988.0421 2015.0421 2010.0959 2077.0168 Mass (m/z) 2211.1045 2234.1028 2298.0840 , P56480 2646.8 2563.2476 , 2691.3960 mitochondrial 2836.4041 3042.5957 3329.4 3713.8579 3845.0930 4012.0 1096.6 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 644.0295 666.0146 717.4493 703.9759 787.4315 855.0472 870.5423 881.2572 917.2670 Carbohydrate kinaselikeprotein 1033.5331 1113.5402 1106.5465 1281.6 1236.6642 1270.1685 1368.6932 1400.6836 1552.8191 1645.8466 1625.8618 4700 ReflectorSpec#1[BP=2212.1,778] 1756.9755 1794.8038 1964.2 1891.0143 Q9D5J6 2050.0471 2065.0532 Mass (m/z) 2140.9192 2156.1602 2204.2209 2211.1055 2300.1746 2284.1809 2402.2478 2477.3723 2646.8 2538.3433 2628.4019 2749.3279 3023.6658 3104.6924 3329.4 3326.7659 , 4012.0 778.2 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 666.0200 679.5151 741.4979 Carbonic anhydrase 842.5089 856.5272 870.5426 903.4647 938.6435 1026.9664 1042.5194 1106.5472