Supporting Information

Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice Ann Wells 1, William T. Barrington 2, Stephen Dearth 3, Amanda May 3, David W. Threadgill 2, Shawn R. Campagna 1, 3, Brynn H. Voy 1, 4 1 University of Tennessee-Knoxville, UT-ORNL Graduate School of Genome Science and Technology, 2 Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, 3 University of Tennessee-Knoxville, Department of Chemistry, 4 University of Tennessee-Knoxville, Department of Animal Science S- 1

Table of contents Table S1: Formulation and composition of experimental diets. Table S2: Significant ANOVA p-values (FDR p<0.05) for liver. Table S3: Significant ANOVA p-values (FDR p<0.05) for muscle. Table S4: Significant ANOVA p-values (FDR p<0.05) for adipose. Tables S5 S11 provided in a separate supplementary file Table S5: Tukey s HSD for liver. Table S6: Tukey s HSD for muscle. Table S7: Tukey s HSD for adipose. Table S8: Number of edges for each node in correlation network analysis. Table S9: Mean values for each factor in liver. Table S10: Mean values for each factor in muscle. Table S11: Mean values for each factor in adipose. S- 2

Table S-1. Diet formulation and composition. Formulation Product # D12052701 D12052702 D12052703 D12052704 D12052705 D12052706 OpenStandard Diet Mediterranean Diet Japanese Hunter-Gatherer Western Ketogenic (Modified) Ingredient gm gm gm gm gm gm Casein 200 44 0 0 38.5 160 Soy Protein Isolate, Supro 661 0 0 16 0 0 0 Fish Protein Isolate 0 27 27 152 8.5 0 Egg White 0 9 6 48 55 0 Beef, Cooked 0 61.9 7 126.5 76.9 0 L-Cystine 3 3 3 3 3 3 Corn Starch 641 0 0 0 30 0 Wheat Starch 0 365 0 0 195 0 Rice Starch 0 0 763.5 0 0 0 Potato Starch 0 0 0 333 30 0 Sucrose 0 61 70 60 205 0 Fructose 0 19 6 29 22 0 Cellulose, BW200 75 40.7 10 75 18.2 37.5 Inulin 25 13.5 38 25 6 12.5 Soybean Oil 70 0 10.5 0 0 0 Corn Oil 0 0 0 0 34.4 8 Menhaden Oil (200 ppm tbhq) 0 13.2 5 24.6 1 8 Trisun Sunflower Oil 0 0 0 0 0 0 Palm Kernal Oil 0 9.9 0 14.7 0 0 Butter, Anhydrous 0 7.4 4.2 0 54.1 161 Lard 0 0 0 0 0 161 Safflower Oil 0 0 0 11.8 0 0 Flaxseed Oil 0 6.1 0 34.4 1 0 Olive Oil 0 117.7 11 0 27.5 0 t-bhq 0.0049 0.0023 0.0039 0 0.0047 0.0033 Mineral Mix S10026 10 10 10 10 10 10 Dicalcium Phosphate 13 13 13 13 13 13 Calcium Carbonate 5.5 5.5 5.5 5.5 5.5 5.5 Potassium Citrate, 1 H2O 16.5 16.5 16.5 16.5 16.5 16.5 Vitamin Mix V10001 10 10 10 10 10 10 Biotin (1%) 0 0.014 0.014 0.1 0.1 0 Choline Bitartrate 2 2 2 2 2 2 Cholesterol 0 0 0.19 0.27 1.5 1.5 Red Wine Extract 0 0.045 0 0 0 0 Green Tea Extract 0 0 0.215 0 0 0 FD&C Red Dye #5 0 0.05 0 0.025 0 0.025 FD&C Yellow Dye #40 0.05 0 0.025 0.025 0 0 FD&C Blue Dye #1 0 0 0.025 0 0.05 0.025 Total 1071.0549 855.5113 1034.6729 994.42 864.7547 609.5533 S- 3

Composition D12052701 D12052702 D12052703 D12052704 D12052705 D12052706 g OpenStandard Diet Mediterranean Diet Japanese Hunter-Gatherer Western Ketogenic Protein 177.0 115.7 120.8 271.1 140.7 142.2 Carbohydrate 570.3 406.7 689.1 362.1 455.3 3.1 Fat 72.4 172.3 44.6 123.2 139.7 339.9 Cholesterol 0.0 0.21 0.23 0.62 1.81 2.09 Fiber 93.8 50.8 50.0 93.8 22.7 46.9 g% Protein 16.5 13.5 11.7 27.3 16.3 23.3 Carbohydrate 53.2 47.5 66.6 36.4 52.6 0.5 Fat 6.8 20.1 4.3 12.4 16.2 55.8 Cholesterol 0.0 0.024 0.023 0.063 0.210 0.342 Fiber 8.8 5.9 4.8 9.4 2.6 7.7 kcal Protein 708 463 483 1084 563 569 Carbohydrate 2281 1627 2757 1448 1821 13 Fat 652 1551 401 1109 1257 3059 Total 3641 3641 3641 3641 3641 3641 kcal% Protein 19 12.71 13 30 15 16 Carbohydrate 63 44.69 76 40 50 0 Fat 18 42.60 11 30 35 84 g% Contribution to Protein sources Casein 98.3 33.1 0.0 0.0 23.8 97.9 Soy Protein Isolate, Supro 661 0.0 0.0 11.5 0.0 0.0 0.0 Fish Protein Isolate 0.0 22.2 21.2 53.3 5.7 0.0 Egg White 0.0 6.3 4.0 14.4 31.7 0.0 Beef, Cooked 0.0 35.8 3.9 31.3 36.6 0.0 Rice Starch 0.0 0.0 56.9 0.0 0.0 0.0 L-Cystine 1.7 2.6 2.5 1.1 2.1 2.1 g% Contribution to Carb sources Corn Starch 100.0 0.0 0.0 0.0 5.9 0.0 Wheat Starch 0.0 80.1 0.0 0.0 38.4 0.0 Rice Starch 0.0 0.0 88.8 0.0 0.0 0.0 Potato Starch 0.0 0.0 0.0 74.7 5.3 0.0 Sucrose 0.0 15.1 10.3 17.0 45.6 0.0 Fructose 0.0 4.7 0.9 8.2 4.9 0.0 Cellulose, BW200 (Insoluble) (g/kg) 70.0 47.6 9.7 75.4 21.0 61.5 Inulin (Soluble) (g/kg) 23.3 15.8 36.7 25.1 6.9 20.5 Total Fiber (g/kg) (includes starch source) 87.5 59.4 48.3 94.3 26.3 76.9 Cholesterol (mg/kg) 37.3 239.8 225.3 627.8 2096.2 3422.9 Red Wine Extract (mg/kg) 0 52.6 0 0 0 0 Green Tea Extract (mg/kg) 0 0 207.8 0 0 0 tbhq (mg/3641 kcals) 4.9 4.9 4.9 4.9 4.9 4.9 Biotin (mg/3641 kcals) 0.20 0.34 0.34 1.20 1.20 0.20 S- 4

Table S2: Significant ANOVA p-values (FDR p<0.05) for liver Compound m/z Retention time Sex Diet Sex by Diet 1-methyl-histidine 168.0779 0.9442287 0.003 0.295 0.242 1-methyladenosine 280.1042 1.282806 0.269 0.008 0.851 2-dehydro-Gluconate 193.0352 5.02352 0.003 0.005 0.22 2-Hydroxy-2-methylbutanedioic 147.0295 11.36092 0.475 0.379 0.234 acid 2-Isopropylmalic acid 175.0609 14.50323 0.757 0.244 0.483 2,3-Diphosphoglyceric acid 264.9521 15.79398 0.434 0.356 0.997 3-hydroxybutyryl-CoA 852.1454 15.96013 0.073 0.018 0.252 3-methylphenylacetic acid 149.0606 15.94347 0.907 0.986 0.824 3-phosphoglycerate 184.9855 12.35473 0.897 0.168 0.717 3-S-methylthiopropionate 119.017 11.32231 0.046 0.035 0.295 4-aminobutyrate 102.0559 4.503228 0.616 0.47 0.646 4-Pyridoxic acid 182.0457 13.30703 0.35 0.025 0.021 6-phospho-Gluconate 275.0166 12.12781 <0.001 <0.001 0.229 Acetyl-CoA 808.1193 16.03261 0.043 0.03 0.437 Acetyllysine 187.109 1.522395 <0.001 0.708 0.22 Aconitate 173.0088 12.78539 0.354 0.263 0.842 Adenine 134.0469 5.625047 0.423 0.32 0.163 Adenosine 266.0896 6.671896 0.293 0.012 0.019 Adenosine 5 -phosphosulfate 426.0118 13.08164 0.564 0.37 0.66 ADP 426.0227 13.10969 0.176 0.134 0.356 ADP-D-glucose 588.0756 12.46579 0.047 0.353 0.41 Alanine 88.04009 1.292004 0.642 0.525 0.42 Allantoate 175.0469 5.242924 <0.001 0.085 0.235 Allantoin 157.0367 1.272447 0.364 0.141 0.095 Aminoadipic acid 160.0611 4.339694 <0.001 0.006 0.234 Aminoimidazole carboxamide 337.055 9.456667 0.626 0.64 0.429 ribonucleotide AMP 346.0551 10.58295 0.958 0.01 0.048 Ascorbic acid 175.0244 5.868752 0.359 0.304 0.318 Asparagine 131.0461 1.104838 0.068 0.036 0.017 Aspartate 132.0298 4.6367 0.079 0.435 0.198 ATP 505.988 14.58165 0.129 0.201 0.428 Atrolactic acid 165.0552 14.22821 0.732 0.34 0.631 Betaine 116.0712 1.449181 0.807 0.002 0.003 Butyryl-CoA 836.1505 16.89659 0.094 0.408 0.119 Carnitine 160.0977 2.148401 0.702 0.881 0.046 CDP 402.0108 12.19754 0.646 0.109 0.07 CDP-ethanolamine 445.0533 5.676858 0.649 0.09 0.123 S- 5

Cellobiose 341.1092 1.235901 0.441 0.172 0.086 Cholesteryl sulfate 465.3047 18.38739 0.604 0.822 0.585 Cholic acid 407.2809 18.04715 0.833 0.34 0.234 Citrate 191.0196 12.48792 0.897 0.738 0.655 Citrate/isocitrate 191.0195 12.48792 0.897 0.738 0.655 Citrulline 174.0882 1.206103 0.05 0.023 0.046 CMP 322.0438 8.719464 0.42 0.358 0.261 Coenzyme A 766.1091 15.90052 0.042 0.069 0.39 Creatine 130.0621 1.24838 0.703 0.013 0.055 Creatinine 112.0513 1.354178 0.557 0.324 0.744 Cyclic-AMP 328.046 11.87003 0.009 0.161 0.275 Cystathionine 221.0598 1.102465 0.499 0.549 0.186 Cysteine 120.0119 1.249641 0.752 0.566 0.422 Cytidine 242.0792 1.186547 0.878 0.105 0.856 damp 330.0608 11.61762 0.371 0.438 0.534 dcmp 306.0498 9.211127 0.904 0.494 0.419 Deoxyinosine 251.0782 5.015367 0.432 0.024 0.011 Deoxyribose-phosphate 213.0168 7.59381 0.001 0.008 0.471 Deoxyuridine 227.067 3.565678 0.712 0.001 0.007 Dephospho-CoA 686.1412 14.54196 0.951 0.001 0.082 dgmp 346.0551 10.57725 0.958 0.01 0.048 Dihydroorotate 157.0253 6.369057 0.547 0.135 0.832 Dihydroxy-acetone-phosphate 168.9904 8.849466 0.005 0.771 0.052 dtmp 321.0494 10.39486 0.889 0.951 0.5 dump 307.0349 6.303688 0.932 0.491 0.104 dutp 466.966 12.46487 0.103 0.526 0.585 FAD 784.1503 14.87661 0.008 0.085 0.668 FMN 455.097 14.27715 0.067 0.451 0.363 Fructose-1,6-bisphosphate 338.9884 12.50127 0.008 0.231 0.503 Fumarate 115.0034 12.21705 0.497 0.001 0.304 GDP 442.016 12.66166 0.378 0.333 0.233 Glucarate 209.0305 11.92858 0.06 0.012 0.165 Gluconate 195.0508 5.186348 <0.001 0.01 0.028 Glucosamine-1/6-phosphate 258.0384 1.78283 0.553 0.764 0.905 Glucose-1/6-phosphate 259.0225 6.137432 0.716 <0.001 0.073 Glutamate 146.0454 4.496096 0.811 <0.001 0.107 Glutamine 145.062 1.147037 <0.001 0.003 0.117 Glutathione 306.077 7.216247 0.711 0.585 0.018 Glutathione disulfide 611.1454 11.53791 0.974 0.797 0.724 Glyceraldehyde-3-phosphate 168.9905 8.893171 0.005 0.771 0.052 Glycerate 105.019 5.659605 0.343 0.087 0.23 Glycerol-3-phosphate 171.0062 6.949478 0.442 0.007 0.072 GMP 362.0509 9.556244 0.884 0.004 0.798 S- 6

GTP 521.9831 14.59963 0.122 0.181 0.379 Guanine 150.0418 2.740335 0.046 0.927 0.201 Guanosine 282.0844 5.200625 0.485 0.507 0.178 Histidine 154.0622 0.914709 0.171 0.011 0.921 Homocysteic acid 182.0125 6.608624 0.023 <0.001 0.403 Homocysteine 134.0278 1.371287 0.699 0.873 0.286 Homoserine 118.0507 1.166061 0.003 0.679 0.073 Hydroxyisocaproic acid 131.0708 13.45274 0.002 0.185 0.24 Hydroxyphenylacetic acid 151.0395 14.38064 0.225 0.624 0.444 Hydroxyproline 130.0508 1.210004 0.381 <0.001 0.255 Hypoxanthine 135.0312 2.585574 0.841 <0.001 0.012 IMP 347.0393 9.546337 0.039 0.777 0.02 Indole 116.0502 7.407636 0.272 0.085 0.402 Inosine 267.0736 4.666428 0.162 0.142 0.012 Isocitrate 191.0196 12.48792 0.897 0.738 0.655 Kynurenic acid 188.0352 13.3591 0.545 0.192 0.295 Kynurenine 207.0776 4.357267 0.627 0.217 0.107 L-arginino-succinate 289.1152 4.557186 0.9 0.131 0.513 Leucine/isoleucine 130.0873 2.147408 0.229 0.056 0.01 Lipoate 205.0354 12.58445 0.394 0.333 0.62 Lysine 145.0978 0.9043637 0.296 0.006 0.034 Malate 133.0138 11.3254 0.553 0.115 0.789 Methionine 148.0434 1.741719 0.045 <0.001 0.111 Methylcysteine 134.0278 1.378434 0.713 0.863 0.283 Myo-inositol 179.0559 6.287088 0.781 0.067 0.231 N-acetyl-glucosamine-1/6-300.0491 7.707054 0.066 0.262 0.987 phosphate N-acetyl-glutamate 188.0562 11.6582 0.743 0.482 0.433 N-acetyl-glutamine 187.0721 6.469678 <0.001 0.011 0.185 N-Acetyl-L-alanine 130.0508 7.569543 <0.001 0.144 0.096 N-acetyl-L-ornithine 173.0932 1.459595 0.531 0.019 0.84 N-carbamoyl-L-aspartate 175.0355 11.13244 0.273 0.204 0.409 NAD+ 662.1016 8.628093 0.758 0.451 0.576 NADH 664.1172 13.13899 0.008 0.036 0.631 NADP+ 742.0687 12.63756 0.415 0.133 0.71 NADPH 744.0842 14.96323 0.363 0.109 0.323 Nicotinate 122.0241 10.40375 0.338 0.577 0.47 Octoluse 8/1P 319.0431 6.710822 0.811 <0.001 0.233 Octoluse bisphosphate 399.0095 12.49189 0.215 0.381 0.185 Ornithine 131.0822 0.9062197 0.421 0.15 0.029 Orotate 155.0097 7.94709 0.789 0.515 0.894 Pantothenate 218.1029 9.972131 0.185 0.074 0.04 Phenylalanine 164.0717 4.411655 0.271 0.67 0.265 S- 7

Phenyllactic acid 165.0551 14.22821 0.732 0.34 0.631 Phenylpyruvate 163.0397 14.73352 0.402 0.481 0.228 Phosphoenolpyruvate 166.9747 12.77026 0.506 0.104 0.787 Pipecolic acid 128.0714 14.98393 0.544 0.271 0.194 Proline 114.0554 1.266749 0.058 0.02 0.038 Propionyl-CoA 822.134 16.58169 0.22 0.062 0.678 Pyroglutamic acid 128.0351 6.540115 0.191 0.986 0.59 Quinolinate 166.0142 12.45207 0.166 0.161 0.183 Riboflavin 375.1307 11.61364 0.001 0.169 0.068 Ribose-phosphate 229.0117 8.179071 0.003 0.349 0.083 S-adenosyl-L-homocysteine 383.1141 5.993446 0.186 0.064 0.577 Sarcosine 88.04008 1.270151 0.64 0.527 0.42 Sedoheptoluse bisphosphate 368.9996 12.52188 0.014 0.149 0.218 Sedoheptulose-1/7-phosphate 289.0323 6.495751 0.35 <0.001 0.122 Serine 104.0351 1.098036 0.058 <0.001 0.022 Shikimate 173.0452 10.6756 0.21 0.188 0.456 Shikimate-3-phosphate 253.0123 11.81871 0.808 0.419 0.749 Succinate 117.0191 10.49904 0.555 0.06 0.611 Taurine 124.0073 1.158478 0.295 0.118 0.038 Taurodeoxycholic acid 498.289 17.89608 0.02 0.113 0.017 Threonine 118.0507 1.166846 0.003 0.679 0.073 Thymidine 241.0825 5.671788 0.319 0.264 0.564 Trehalose/sucrose 341.1092 1.232476 0.616 0.274 0.095 Tryptophan 203.0822 7.427441 0.235 0.015 0.223 Tyrosine 180.0664 2.589614 0.545 0.108 0.475 UDP 402.9944 12.54567 0.524 0.503 0.23 UDP-D-glucose 565.047 12.10283 0.997 0.058 0.245 UDP-D-glucuronate 579.0271 14.47537 0.329 0.025 0.229 UDP-N-acetyl-glucosamine 606.0751 12.14877 0.853 0.521 0.812 UMP 323.028 9.232733 0.093 0.67 0.627 Uracil 111.0195 1.845335 0.029 0.027 0.535 Uric acid 167.0211 5.536854 0.059 0.64 0.662 Uridine 243.0623 1.769847 <0.001 0.272 0.109 UTP 482.9609 14.45184 0.359 0.652 0.22 Valine 116.0712 1.450758 0.822 0.002 0.003 Xanthine 151.0257 2.856254 0.926 0.019 0.004 Xanthosine 283.068 7.474506 0.371 0.01 0.005 Xanthosine-5-phosphate 363.0349 9.67898 0.425 0.234 0.951 Xanthurenic acid 204.03 13.19724 0.114 0.047 0.287 α -ketoglutarate 145.0139 11.92772 0.97 0.498 0.527 S- 8

Table S3: Significant ANOVA p-values (FDR p<0.05) for muscle Compound m/z Retention time Sex Diet Sex by Diet 1-Methyl-Histidine 168.0779 0.9169151 0.076 0.185 0.986 2-dehydro-D-gluconate 193.0352 4.946577 0.433 0.979 0.596 2-Hydroxy-2-147.0295 11.38942 0.570 0.975 0.901 methylbutanedioic acid 2-Isopropylmalic acid 175.0609 14.49654 0.911 0.348 0.987 2-oxo-4-methylthiobutanoate 147.012 12.47061 0.171 0.781 0.617 2-oxobutanoate 101.024 8.943554 0.998 0.686 0.275 3-methylphenylacetic acid 149.0606 16.54142 0.833 0.938 0.444 3-phosphoglycerate 184.9855 12.42114 0.546 0.974 0.453 3-S-methylthiopropionate 119.017 11.45267 0.710 0.955 0.894 4-aminobutyrate 102.0559 4.459141 0.825 0.536 0.635 6-phospho-D-gluconate 275.0173 12.21901 0.361 0.747 0.646 Acetyl CoA 101.024 7.42638 0.216 0.810 0.718 Acetyllysine 808.1192 16.25955 0.045 0.026 0.799 Aconitate 187.109 1.532926 0.607 0.803 0.781 Adenosine 173.0087 12.85596 0.331 0.301 0.965 ADP 266.0897 6.686973 0.679 0.549 0.874 ADP-D-glucose 426.0225 13.17548 0.600 0.496 0.762 Aetoacetate 588.0753 12.56403 0.582 0.781 0.944 Allantoate 175.0469 5.267753 0.794 0.491 0.955 Allantoin 157.0367 1.283768 0.794 0.766 0.712 Aminoadipic acid 160.0611 4.304269 0.001 0.003 0.360 AMP 346.0553 10.68014 0.177 0.442 0.802 Arginine 173.1041 0.883432 0.347 0.072 0.870 Ascorbic acid 175.0242 5.919798 0.679 0.665 0.393 Asparagine 131.0462 1.102234 0.862 0.484 0.539 Aspartate 132.0298 4.62583 0.439 0.225 0.812 ATP 505.9884 14.64614 0.953 0.645 0.854 Atrolactic acid 165.0551 14.51391 0.682 0.707 0.661 Betaine 116.0714 1.446598 0.584 0.080 0.922 CDP 402.0113 12.31058 0.708 0.970 0.444 CDP-ethanolamine 445.054 5.696146 0.540 0.293 0.983 Cholic acid 407.2812 18.13667 0.949 0.262 0.564 Citraconic acid 129.0191 11.72099 0.638 0.578 0.343 Citrate 191.0196 12.5682 0.638 0.907 0.604 Citrate/isocitrate 191.0196 12.5682 0.638 0.907 0.604 Citrulline 174.0882 1.218019 0.470 0.135 0.213 CMP 322.0444 8.807094 0.195 0.538 0.818 Creatine 130.0621 1.241876 0.190 0.609 0.523 S- 9

CTP 481.9768 14.47774 0.720 0.500 0.441 Cyclic AMP 328.0462 11.87123 0.063 0.600 0.660 Cystathionine 221.0602 1.255307 0.451 0.477 0.809 Cysteine 120.0119 1.254725 0.161 0.538 0.769 Cytidine 242.0782 1.929419 0.571 0.442 0.752 Deoxyribose-phosphate 213.017 9.7429 0.019 0.311 0.701 Deoxyuridine 227.067 3.546488 0.006 0.679 0.201 dgmp 346.0553 10.68308 0.177 0.442 0.802 Dihydroxy-acetone-phosphate 168.9904 8.877982 0.684 0.362 0.580 Dimethylglycine 102.0559 1.002885 0.589 0.821 0.838 Erythrose-4-phosphate 199.0013 6.129674 0.014 0.029 0.250 FAD 784.1509 14.92712 0.851 0.825 0.980 Fructose-1,6-bisphosphate 338.9886 12.56047 0.383 0.447 0.871 Fumarate 115.0034 11.45089 0.354 0.814 0.889 GDP 442.0168 12.76409 0.984 0.538 0.889 Glucarate 209.0302 11.96993 0.675 0.938 0.941 Gluconate 195.0508 5.255502 0.271 0.830 0.343 Glucono-δ-lactone-6-257.0071 6.346225 0.136 0.283 0.532 phosphate Glucosamine-1/6-phosphate 258.0387 1.560598 0.803 0.941 0.700 Glucose-1/6-phosphate 259.0228 6.173521 0.017 0.126 0.345 Glutamate 146.0454 4.469115 0.379 0.279 0.870 Glutamine 145.062 1.109982 0.078 0.578 0.912 Glutathione 306.0769 7.220196 0.288 0.640 0.716 Glutathione disulfide 611.1461 11.56326 0.885 0.575 0.647 Glyceraldehdye-3-phosphate 168.9904 8.908275 0.603 0.432 0.703 Glycerate 105.019 5.693265 0.745 0.750 0.919 Glycerol-3-phosphate 171.0062 7.006114 0.220 0.442 0.568 GMP 362.0511 9.595345 0.951 0.677 0.823 GTP 521.9835 14.64214 0.487 0.800 0.487 Guanine 150.0418 2.717246 0.850 0.820 0.787 Histidine 154.0623 0.9123318 0.872 0.033 0.129 Homocysteic acid 182.0126 6.635017 0.076 <0.001 0.129 Homocysteine 134.0279 1.361354 0.689 0.114 0.617 Homoserine 118.0507 1.227774 0.855 0.004 0.277 Hydroxyisocaproic acid 131.0708 13.45946 0.343 0.686 0.736 Hydroxyphenylacetic acid 151.0395 14.43982 0.024 0.781 0.592 Hydroxyproline 130.0508 1.162459 0.078 <0.001 0.129 Hypoxanthine 135.0312 2.560346 0.728 0.538 0.628 IMP 347.0395 9.593002 0.115 0.892 0.736 Indole 116.0502 7.413458 0.882 0.375 0.663 Inosine 267.0737 4.695882 0.060 0.622 0.771 Isocitrate 191.0195 12.5682 0.638 0.907 0.604 S- 10

Kynurenic acid 188.0352 14.48016 0.998 0.640 0.368 Kynurenine 207.0776 4.34457 0.010 0.848 0.944 Lactate 89.02431 6.136123 0.737 0.662 0.953 Leucine/isoleucine 130.0873 2.120031 0.822 0.101 0.964 Lipoate 205.0354 12.54339 0.987 0.464 0.536 Lysine 145.0978 0.864782 0.125 0.089 0.384 Malate 133.0139 11.45263 0.444 0.810 0.887 Methionine 148.0434 1.732659 0.042 0.145 0.658 Methylcysteine 134.0279 1.367612 0.640 0.170 0.637 Methylmalonic acid 117.0191 10.46987 0.640 0.310 0.621 Myo-inositol 179.0556 6.263708 0.497 0.791 0.914 N-acetyl-glucosamine-1/6-300.0494 7.338713 0.117 0.736 0.614 phosphate N-acetyl-glutamate 188.0562 11.63871 0.946 0.625 0.816 N-acetyl-glutamine 187.0723 6.460396 0.005 0.985 0.374 N-acetyl-L-alanine 130.0508 7.552967 0.046 0.902 0.677 N-acetyl-L-ornithine 173.0932 1.428486 0.705 0.200 0.553 N-carbamoyl-L-aspartate 175.0358 11.25711 0.799 0.887 0.294 NAD+ 662.1017 8.6356 0.955 0.616 0.549 NADH 664.1174 13.17502 0.682 0.497 0.922 NADP+ 742.0695 12.69483 0.713 0.804 0.677 NADPH 744.085 15.11565 0.983 0.609 0.578 Nicotinate 122.0241 10.37855 0.717 0.840 0.812 Ornithine 131.0822 1.142626 0.599 0.861 0.523 Orotate 155.0097 7.945485 <0.001 0.999 0.457 P-hydroxybenzoate 137.0239 10.36727 0.997 0.963 0.802 Pantothenate 218.103 9.942012 <0.001 0.180 0.487 Phenylalanine 164.0717 4.35183 0.482 0.244 0.992 Phenyllactic acid 165.0551 14.51003 0.742 0.730 0.685 Phosphoenolpyruvate 166.9747 12.83701 0.633 0.962 0.552 Proline 114.0554 1.276638 0.817 0.047 0.490 Pyroglutamic acid 128.0351 6.532551 0.969 0.958 0.863 Pyrophosphate 176.9356 12.68955 0.892 0.896 0.663 Quinolinate 166.0142 14.03343 0.174 0.444 0.345 Ribose-phosphate 229.0117 7.742831 0.235 0.645 0.661 Sedoheptulose-1/7-phosphate 289.033 6.474514 0.413 0.606 0.592 Serine 104.0351 1.105778 0.438 0.456 0.732 Shikimate 173.0452 10.65361 0.996 0.985 0.523 Shikimate-3-phosphate 253.0124 11.83869 0.865 0.887 0.833 Succinate 117.0191 10.47085 0.640 0.310 0.621 Taurine 124.0073 1.156293 0.897 0.612 0.988 Taurodeoxycholic acid 498.289 17.95588 0.062 0.778 0.549 Threonine 118.0507 1.228258 0.837 0.004 0.271 S- 11

Thymidine 241.0827 5.704769 0.145 0.303 0.981 Thymine 125.0352 3.363783 0.975 0.793 0.619 Trehalose/sucrose 341.1092 1.318694 0.570 0.385 0.619 Tryptophan 203.0822 7.431092 0.017 0.030 0.250 Tyrosine 180.0664 2.579143 0.110 0.092 0.533 UDP 402.9948 12.60474 0.487 0.877 0.847 UDP-D-glucose 565.0472 12.14668 0.842 0.762 0.979 UDP-D-glucuronate 579.0272 14.55233 0.924 0.736 0.704 UDP-N-acetyl-glucosamine 606.0746 12.18459 0.700 0.445 0.787 UMP 323.0281 9.285866 0.555 0.834 0.845 Uracil 111.0195 1.844732 0.908 0.960 0.581 Uric acid 167.021 5.541261 0.493 0.347 0.870 Uridine 243.0624 1.764417 0.895 0.645 0.768 UTP 482.9611 14.53945 0.823 0.542 0.473 Valine 116.0714 1.443583 0.867 0.029 0.399 Xanthine 151.0257 2.832925 0.254 0.689 0.679 Xanthosine 283.068 7.400645 0.965 0.943 0.537 α-ketoglutarate 145.0139 11.83516 0.827 0.822 0.233 S- 12

Table S4: Significant ANOVA p-values (FDR p<0.05) for adipose Compound m/z Retention time Sex Diet Sex by Diet 1-Methyl-Histidine 168.0779 6.279245 0.896 0.73 0.96 1-Methyladenosine 280.1046 1.271327 0.04 0.504 0.514 2-dehydro-Gluconate 193.0352 4.929214 0.814 0.873 0.71 2-Hydroxy-2-147.0295 11.54736 0.506 0.076 0.379 methylbutanedioic acid 2-Isopropylmalic acid 175.0609 14.6273 0.955 0.937 0.968 3-methylphenylacetic acid 149.0606 16.13234 0.88 0.05 0.896 3-phospho-serine 184.0014 8.763332 0.584 0.494 0.882 3-phosphoglycerate 184.9855 12.46848 0.734 0.601 0.628 3-S-methylthiopropionate 119.017 11.48507 0.933 0.569 0.759 4-aminobutyrate 102.0559 4.571528 0.94 0.385 0.063 4-Pyridoxic acid 182.0456 13.46533 0.745 0.134 0.9 6-phospho-Gluconate 275.0172 12.25922 0.936 0.357 0.747 Acadesine 257.0882 1.204447 0.652 0.653 0.997 Acetyl-CoA 808.1193 16.36466 0.479 0.522 0.54 Acetyllysine 187.109 1.567012 0.812 0.811 0.912 Aconitate 173.0089 12.90448 0.634 0.868 0.589 Adenosine 266.0897 6.681546 0.006 0.201 0.668 ADP 426.0229 13.20947 0.695 0.284 0.807 ADP-D-glucose 588.0751 12.52872 0.321 0.418 0.828 Alanine 88.03996 1.204036 0.1 0.336 0.639 Allantoin 157.0367 1.279093 0.781 0.47 0.915 Aminoadipic acid 160.0611 4.458091 0.856 0.336 0.89 AMP 346.0554 10.69433 0.815 0.337 0.663 Arginine 173.104 0.6989767 0.861 0.191 0.313 Ascorbic acid 175.0241 5.912348 0.937 0.505 0.838 Asparagine 131.046 1.134015 0.949 0.132 0.64 Aspartate 132.0298 4.673595 0.861 0.337 0.979 ATP 505.9893 14.65705 0.739 0.569 0.925 CDP 402.0113 12.31668 0.609 0.778 0.712 CDP-ethanolamine 445.054 5.674383 0.539 0.892 0.76 Cellobiose 341.1093 1.296405 0.778 0.582 0.706 Citrate 191.0196 12.61023 0.518 0.925 0.759 Citrate/isocitrate 191.0195 12.61023 0.518 0.925 0.759 Citrulline 174.088 1.220223 0.04 0.358 0.696 CMP 322.0444 8.791982 0.725 0.932 0.885 Creatine 130.062 1.24981 0.152 0.653 0.589 Creatinine 112.0512 1.290821 0.932 0.7 0.379 Cyclic-AMP 328.0462 11.95169 0.936 0.656 0.751 S- 13

Cysteine 120.0122 1.247594 0.923 0.649 0.266 Cytidine 242.0781 1.934583 0.087 0.377 0.919 Deoxyuridine 227.0671 3.673078 0.828 0.583 0.874 dgmp 346.0554 10.69433 0.815 0.337 0.663 Dihydroorotate 157.0252 6.360754 0.677 0.769 0.512 Dihydroxy-acetone-phosphate 168.9903 9.058042 0.486 0.188 0.871 Dimethylglycine 102.0559 4.578036 0.845 0.341 0.555 dump 307.035 6.348562 0.292 0.512 0.97 Erythrose-4-phosphate 199.0015 6.041022 0.798 0.713 0.772 FAD 784.1503 14.96925 0.287 0.911 0.918 Fructose-1,6-bisphosphate 338.9885 12.6943 0.845 0.484 0.733 Fumarate 115.0035 11.21387 0.698 0.337 0.844 GDP 442.0166 12.74839 0.689 0.789 0.942 Glucarate 209.0304 11.94075 0.845 0.618 0.972 Gluconate 195.0508 5.196307 0.97 0.396 0.871 Glucosamine-1/6-phosphate 258.0388 4.762531 0.695 0.043 0.032 Glucose-1/6-phosphate 259.0227 6.325644 0.852 0.226 0.836 Glutamate 146.0454 4.585854 0.641 0.129 0.469 Glutamine 145.062 1.163747 0.95 0.086 0.016 Glutathione 306.0771 7.332019 0.988 0.552 0.469 Glutathione disulfide 611.1464 11.65822 0.343 0.494 0.306 Glyceraldehyde-3-phosphate 168.9903 9.035762 0.871 0.577 0.504 Glycerate 105.019 5.721847 0.821 0.461 0.596 Glycerol-3-phosphate 171.006 7.234438 0.999 0.969 0.738 GMP 362.051 9.635168 0.806 0.917 0.941 GTP 521.9834 14.57753 0.816 0.521 0.918 Guanidoacetic acid 116.0461 1.244228 0.609 0.11 0.908 Guanine 150.0418 2.759581 0.39 0.204 0.73 Guanosine 282.085 5.131655 0.006 0.338 0.648 Histidine 154.0624 1.141304 0.656 0.453 0.767 Homocysteic acid 182.0126 5.225487 0.785 0.289 0.306 Homocysteine 134.028 1.323767 0.983 0.569 0.388 Homoserine 118.0507 1.179999 0.924 0.068 0.248 Hydroxyisocaproic acid 131.0708 13.72845 0.317 0.983 0.555 Hydroxyphenylacetic acid 151.0395 14.43036 0.507 0.632 0.665 Hydroxyphenylpyruvate 179.035 13.33573 0.708 0.337 0.712 Hydroxyproline 130.0508 1.18329 0.95 <0.001 0.767 Hypoxanthine 135.0312 2.635298 0.415 0.494 0.824 IMP 347.0395 9.64838 0.931 0.2 0.683 Inosine 267.0737 4.632779 0.037 0.444 0.95 Isocitrate 191.0196 12.61023 0.518 0.925 0.759 Lactate 89.02441 6.038192 0.849 0.521 0.663 Leucine/isoleucine 130.0872 2.215075 0.998 0.536 0.79 S- 14

Lipoate 205.0353 12.58044 0.798 0.86 0.925 Lysine 145.0979 0.8822759 0.618 0.453 0.95 Malate 133.0138 11.48782 0.998 0.103 0.584 Methionine 148.0435 1.770768 0.577 0.177 0.884 Methionine sulfoxide 164.0388 1.77801 0.688 0.731 0.44 Methylcysteine 134.028 1.363579 0.964 0.377 0.588 Methylmalonic acid 117.019 10.72931 0.939 0.461 0.476 Myo-inositol 179.0559 6.304824 0.708 0.336 0.934 N-acetyl-glucosamine-1/6-300.0494 7.626842 0.28 0.958 0.985 phosphate N-acetyl-glutamate 188.0562 11.83087 0.001 0.163 0.588 N-acetyl-glutamine 187.0722 6.423823 0.28 0.719 0.664 N-Acetyl-L-alanine 130.0508 7.673829 0.781 0.41 0.15 N-acetyl-L-ornithine 173.0932 1.520715 0.293 0.46 0.603 N-carbamoyl-L-aspartate 175.0357 11.31352 0.676 0.781 0.526 NAD+ 662.1017 8.666221 0.652 0.318 0.853 NADH 664.1174 13.26132 0.928 0.713 0.506 NADP+ 742.0699 12.7467 0.33 0.629 0.818 NADPH 744.0851 15.39257 0.437 0.222 0.755 Nicotinate 122.0241 10.53017 0.317 0.648 0.708 Octoluse 8/1P 319.0437 7.955659 0.212 0.086 0.41 Ornithine 131.0822 1.177075 0.51 0.056 0.74 Orotate 155.0097 7.999317 0.53 0.884 0.678 Pantothenate 218.1031 10.14107 <0.001 0.369 0.848 Phenylalanine 164.0717 4.497637 0.72 0.752 0.4 Phosphoenolpyruvate 166.9749 12.88426 0.907 0.676 0.967 Proline 114.0554 1.258988 0.148 0.05 0.024 Pyroglutamic acid 128.0351 6.567471 0.426 0.46 0.392 Pyrophosphate 176.9356 12.70072 0.59 0.981 0.878 Quinolinate 166.0143 14.11953 0.801 0.898 0.752 Ribose-phosphate 229.0117 6.728639 0.973 0.83 0.722 S-adenosyl-L-homoCysteine 383.1132 10.14317 <0.001 0.337 0.788 Sarcosine 88.03998 1.208019 0.1 0.336 0.639 Sedoheptulose-1/7-phosphate 289.0329 6.760711 0.708 0.628 0.895 Serine 104.0351 1.126813 0.933 0.373 0.379 Shikimate 173.0452 10.81524 0.6 0.087 0.754 Shikimate-3-phosphate 253.0123 11.97721 0.85 0.955 0.651 Succinate 117.0191 10.72931 0.717 0.35 0.937 Taurine 124.0072 1.155703 0.948 0.601 0.512 Taurodeoxycholic acid 498.2892 17.96274 0.599 0.279 0.712 Threonine 118.0507 1.182911 0.891 0.071 0.651 Thymidine 241.0827 5.60485 0.968 0.759 0.918 Thymine 125.0352 3.545883 0.954 0.694 0.919 S- 15

Trehalose/sucrose 341.1093 1.304547 0.966 0.167 0.803 Tryptophan 203.0822 7.430562 0.505 0.095 0.853 Tyrosine 180.0664 2.655322 0.986 0.11 0.772 UDP 402.995 12.64768 0.601 0.343 0.865 UDP-D-glucose 565.0472 12.20336 0.569 0.932 0.929 UDP-D-glucuronate 579.0279 14.54791 0.708 0.707 0.879 UDP-N-acetyl-glucosamine 606.0757 12.25692 0.809 0.492 0.96 UMP 323.0282 9.326558 0.972 0.584 0.973 Uracil 111.0195 1.895311 0.861 0.284 0.963 Uric acid 167.021 5.518082 0.526 0.11 0.628 Uridine 243.0624 1.801348 0.423 0.843 0.788 UTP 482.9611 14.4932 0.897 0.951 0.792 Valine 116.0714 1.484647 0.577 0.284 0.776 Xanthine 151.0258 2.924532 0.952 0.459 0.804 Xanthosine 283.0682 7.551906 0.834 0.337 0.715 α -ketoglutarate 145.0139 12.01192 0.28 0.04 0.881 S- 16