#METABOLOMICS WORKBENCH mhandzlik_20221111_111600 DATATRACK_ID:3566 STUDY_ID:ST002340 ANALYSIS_ID:AN003823 PROJECT_ID:PR001502 VERSION 1 CREATED_ON November 11, 2022, 4:49 pm #PROJECT PR:PROJECT_TITLE Serine and lipid metabolism PR:PROJECT_SUMMARY We analyzed hepatic and paw skin lipid metabolites in mice (BKS-db/db) in PR:PROJECT_SUMMARY response to dietary serine supplementation. PR:INSTITUTE Salk Institute for Biological Studies PR:DEPARTMENT Molecular and Cell Biology Laboratory PR:LABORATORY Metallo Lab PR:LAST_NAME Handzlik PR:FIRST_NAME Michal PR:ADDRESS 10010 N Torrey Pines Rd, La Jolla, California, 92037, USA PR:EMAIL mhandzlik@salk.edu PR:PHONE 2069601945 PR:FUNDING_SOURCE R01CA234245 #STUDY ST:STUDY_TITLE Serine supplementation and hepatic and skin sphingolipid diversity ST:STUDY_SUMMARY We analyzed hepatic and paw skin lipid metabolites in mice (BKS-db/db) in ST:STUDY_SUMMARY response to dietary serine supplementation. ST:INSTITUTE Salk Institute for Biological Studies ST:DEPARTMENT Molecular and Cell Biology Laboratory ST:LABORATORY Metallo Lab ST:LAST_NAME Handzlik ST:FIRST_NAME Michal ST:ADDRESS 10010 N Torrey Pines Rd, La Jolla, California, 92037, USA ST:EMAIL mhandzlik@salk.edu ST:PHONE 2069601945 ST:NUM_GROUPS Control and serine supplemented ST:TOTAL_SUBJECTS 16 ST:NUM_MALES 16 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:GENOTYPE_STRAIN BKS-db/db SU:AGE_OR_AGE_RANGE 14-week-old SU:WEIGHT_OR_WEIGHT_RANGE 40-50 SU:GENDER Male SU:ANIMAL_ANIMAL_SUPPLIER JAX SU:ANIMAL_HOUSING 5/cage SU:ANIMAL_LIGHT_CYCLE 12h dark/12 h light SU:ANIMAL_FEED Special diets; see group labeling SU:ANIMAL_WATER Ad libitum #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - S_481 Group:Control diet RAW_FILE_NAME=S_481.d SUBJECT_SAMPLE_FACTORS - S_482 Group:Control diet RAW_FILE_NAME=S_482.d SUBJECT_SAMPLE_FACTORS - S_483 Group:Control diet RAW_FILE_NAME=S_483.d SUBJECT_SAMPLE_FACTORS - S_485 Group:Control diet RAW_FILE_NAME=S_485.d SUBJECT_SAMPLE_FACTORS - S_486 Group:Control diet RAW_FILE_NAME=S_486.d SUBJECT_SAMPLE_FACTORS - S_487 Group:Control diet RAW_FILE_NAME=S_487.d SUBJECT_SAMPLE_FACTORS - S_488 Group:Control diet RAW_FILE_NAME=S_488.d SUBJECT_SAMPLE_FACTORS - S_489 Group:Control diet RAW_FILE_NAME=S_489.d SUBJECT_SAMPLE_FACTORS - S_490 Group:Serine supplemented diet RAW_FILE_NAME=S_490.d SUBJECT_SAMPLE_FACTORS - S_491 Group:Serine supplemented diet RAW_FILE_NAME=S_491.d SUBJECT_SAMPLE_FACTORS - S_492 Group:Serine supplemented diet RAW_FILE_NAME=S_492.d SUBJECT_SAMPLE_FACTORS - S_493 Group:Serine supplemented diet RAW_FILE_NAME=S_493.d SUBJECT_SAMPLE_FACTORS - S_494 Group:Serine supplemented diet RAW_FILE_NAME=S_494.d SUBJECT_SAMPLE_FACTORS - S_497 Group:Serine supplemented diet RAW_FILE_NAME=S_497.d SUBJECT_SAMPLE_FACTORS - S_498 Group:Serine supplemented diet RAW_FILE_NAME=S_498.d SUBJECT_SAMPLE_FACTORS - S_499 Group:Serine supplemented diet RAW_FILE_NAME=S_499.d SUBJECT_SAMPLE_FACTORS - L_481 Group:Control diet RAW_FILE_NAME=L_481.d SUBJECT_SAMPLE_FACTORS - L_482 Group:Control diet RAW_FILE_NAME=L_482.d SUBJECT_SAMPLE_FACTORS - L_483 Group:Control diet RAW_FILE_NAME=L_483.d SUBJECT_SAMPLE_FACTORS - L_485 Group:Control diet RAW_FILE_NAME=L_485.d SUBJECT_SAMPLE_FACTORS - L_486 Group:Control diet RAW_FILE_NAME=L_486.d SUBJECT_SAMPLE_FACTORS - L_487 Group:Control diet RAW_FILE_NAME=L_487.d SUBJECT_SAMPLE_FACTORS - L_488 Group:Control diet RAW_FILE_NAME=L_488.d SUBJECT_SAMPLE_FACTORS - L_489 Group:Control diet RAW_FILE_NAME=L_489.d SUBJECT_SAMPLE_FACTORS - L_490 Group:Serine supplemented diet RAW_FILE_NAME=L_490.d SUBJECT_SAMPLE_FACTORS - L_491 Group:Serine supplemented diet RAW_FILE_NAME=L_491.d SUBJECT_SAMPLE_FACTORS - L_492 Group:Serine supplemented diet RAW_FILE_NAME=L_492.d SUBJECT_SAMPLE_FACTORS - L_493 Group:Serine supplemented diet RAW_FILE_NAME=L_493.d SUBJECT_SAMPLE_FACTORS - L_494 Group:Serine supplemented diet RAW_FILE_NAME=L_494.d SUBJECT_SAMPLE_FACTORS - L_497 Group:Serine supplemented diet RAW_FILE_NAME=L_497.d SUBJECT_SAMPLE_FACTORS - L_498 Group:Serine supplemented diet RAW_FILE_NAME=L_498.d SUBJECT_SAMPLE_FACTORS - L_499 Group:Serine supplemented diet RAW_FILE_NAME=L_499.d #COLLECTION CO:COLLECTION_SUMMARY Liver and paw skin samples were collected using Wollenberger clamps pre-cooled CO:COLLECTION_SUMMARY to the temperature of liquid nitrogen and stored at -80 C until analysis. CO:SAMPLE_TYPE Liver CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY BKS-db/db mice were subjected to a dietary intervention that consisted of a TR:TREATMENT_SUMMARY control diet or serine supplemented diet. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Samples were extracted with 400 ul of methanol (-20 C), 100 ul of water SP:SAMPLEPREP_SUMMARY (ice-cold), 400 saline (ice-cold), and 1000 ul of chloroform (-20 C). SP:PROCESSING_STORAGE_CONDITIONS Room temperature SP:EXTRACT_STORAGE 4℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The gradient elution program consisted of the following profile: 0 min, 82% B; 3 CH:CHROMATOGRAPHY_SUMMARY min, 82% B; 4 min, 90% B, 18 min, 99% B; 25 min, 99%, 27 min, 82% B, 30 min, 82% CH:CHROMATOGRAPHY_SUMMARY B. Column re-equilibration followed each sample and lasted 10 min. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME 6460C CH:COLUMN_NAME Peeke Scientific Spectra 3 μm C8SR 150 × 3 mm CH:FLOW_RATE 0.5 ml/min CH:COLUMN_TEMPERATURE 40 CH:SOLVENT_A 100% HPLC-grade water containing 2 mM ammonium formate and 0.2% formic acid CH:SOLVENT_B 100% methanol containing 0.2% formic acid and 1 mM ammonium formate #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6460 QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Mass Hunter Quantifier #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS normalized ion count/mg protein MS_METABOLITE_DATA_START Samples S_481 S_482 S_483 S_485 S_486 S_487 S_488 S_489 S_490 S_491 S_492 S_493 S_494 S_497 S_498 S_499 Factors Group:Control diet Group:Control diet Group:Control diet Group:Control diet Group:Control diet Group:Control diet Group:Control diet Group:Control diet Group:Serine supplemented diet Group:Serine supplemented diet Group:Serine supplemented diet Group:Serine supplemented diet Group:Serine supplemented diet Group:Serine supplemented diet Group:Serine supplemented diet Group:Serine supplemented diet Cer 18:1/16:0 965.1240075 867.3127631 924.8103029 706.4825894 948.3575211 808.3095698 1076.222589 679.6352913 1065.23927 891.0854256 1437.983599 662.1077368 1161.38673 608.0746412 807.5925071 787.0410908 Cer 18:1/18:0 564.333097 507.6289663 626.2570099 508.8757998 655.8160282 470.0063396 586.8901163 476.1005689 669.4707256 510.2245464 756.5000649 359.9455833 600.1946318 389.8751601 483.7775353 390.8804578 Cer 18:1/18:1 1220.062725 1050.728786 1418.067469 831.1586084 1319.264419 929.7898942 1053.680586 833.453866 628.3591492 1047.794405 904.1186733 808.8458973 819.4117959 667.3831755 1006.447677 757.9509634 Cer 18:1/20:0 872.835544 779.006807 878.3075167 679.5317536 1059.704672 760.9588909 1138.4437 647.2353608 1025.059667 742.0229943 1126.534317 593.7812226 943.1940947 651.0439635 885.5003732 795.9200446 Cer 18:1/22:0 1031.806577 717.1601904 821.2201205 915.92743 873.4112847 719.3161526 1101.625095 601.8363416 1120.970134 834.7170257 1217.716972 603.479639 1006.926194 765.900559 868.3173053 829.193998 Cer 18:1/23:0 222.080563 137.1785487 152.4481685 197.7048088 179.3308141 150.6297156 239.7380883 114.8356194 208.800485 165.0797476 246.5193496 95.6968092 163.0537714 124.6478506 169.5820444 131.9208025 Cer 18:1/24:0 1872.659971 1264.797723 959.1509917 1625.457527 1306.948929 1497.519752 1590.610369 398.1919021 2248.287609 1323.552963 2034.782575 717.331721 1739.68846 887.760926 1112.559838 1462.264393 DHCer 18:0/16:0 8.147182033 9.462098272 9.134785401 5.418899167 11.3267688 7.488752742 5.823344031 6.460197702 7.926924282 5.323656894 11.71984005 7.700623537 8.364282153 4.977126113 4.967436651 5.102256985 DHCer 18:0/18:0 21.1890984 22.44161727 23.94795092 18.56726366 28.70624618 20.15365508 17.2659851 19.80334676 33.26021658 21.68157721 25.17894152 22.47717624 23.3127168 16.0612532 21.00917074 13.67166226 DHCer 18:0/20:0 34.97813985 39.81622718 33.78810482 28.87206552 38.77434023 38.63263435 33.32884004 28.02168622 57.50895042 30.27298999 44.46233896 38.27594232 34.89157325 29.33440675 30.41573932 28.42410569 DHCer 18:0/22:0 15.25222517 14.74159936 14.63742815 14.11505586 16.32147771 12.95076412 14.13260724 5.74883945 17.51864049 12.11854891 25.32398616 11.43893891 14.46541969 13.07192229 9.220115164 17.61505302 DHCer 18:0/23:0 11.91340327 11.82342566 10.33648744 12.51525331 12.07194715 11.23958964 8.621009761 2.816288467 18.38130443 8.982495098 19.70111749 7.447532903 11.65075982 12.60788338 9.671021864 11.86052808 DHCer 18:0/24:0 28.60398251 20.9623717 23.80636494 22.17037677 28.78101033 26.83197769 20.52986377 3.420748334 31.88167175 26.80382018 58.7695162 21.41252852 38.22591331 20.83629938 22.50007581 24.06842965 DHCer 18:0/24:1 6.83109335 6.705561957 7.035328686 6.079961161 6.527808669 6.041061307 6.148577281 6.527745698 8.42764467 4.995652376 13.11963757 5.220638424 8.854652108 6.116242149 4.936140404 7.065265641 doxCer 18:1/18:0 17.76963052 14.21783905 13.11079621 19.49691809 12.31008811 15.25796659 28.57911413 23.0262757 17.5641007 27.78587935 11.82725252 11.27580843 8.106584773 7.75323656 8.217735026 7.399128229 doxCer 18:1/20:0 118.6163983 108.6691266 68.73101876 115.9612174 75.99953479 99.96254443 144.0148977 104.2216846 89.17158817 77.65441128 57.00255886 83.96304826 79.86202629 79.65365813 82.73220799 50.1567483 doxCer 18:1/22:0 49.71992524 44.08415032 44.75982804 56.87789222 31.80961339 52.21241476 77.45121301 50.82285919 48.63904809 61.43189962 39.15703671 25.2230065 39.82215695 38.6566119 39.98480028 32.20218598 doxCer 18:1/22:1 47.08660085 49.23639628 39.95014597 43.13737682 37.55684189 47.36644673 54.96621279 38.41051832 35.89473515 40.04932566 42.42905608 53.0817841 49.57439124 31.03924325 48.87420519 31.61222227 doxCer 18:1/24:0 57.88004538 34.65475361 34.43445551 50.84970891 42.98538009 49.4372834 60.45402455 28.55029212 33.67785337 57.81080327 29.50432436 20.72489519 31.66434574 25.09611789 23.15800951 19.27706431 doxCer 18:1/24:1 59.29227177 33.1847903 49.81771619 52.36900714 56.0192733 43.80818171 68.22194696 64.51841285 34.64291385 137.8611733 46.69135899 36.22404342 27.92481532 19.08724998 29.09790753 19.30164613 doxDHCer 18:0/18:0 0.958941942 0.545939774 0.873279508 1.041192968 0.864714051 1.111743901 1.008785829 1.126852075 0.55372911 0.977814532 0.660664505 0.54315978 0.422528309 0.408874762 0.363879059 0.242369139 doxDHCer 18:0/20:0 5.875564013 3.477348381 5.622457213 4.638410999 5.882315858 4.461361939 5.609594374 5.028011853 2.247569811 2.705058486 4.461662143 3.488558868 1.989362957 1.740263777 2.712542041 1.986395989 doxDHCer 18:0/22:0 8.45055083 4.37192983 5.501504372 6.483875731 6.595618015 6.599197773 8.000136382 4.271516389 3.21360076 3.119305572 4.909431705 3.396112588 2.513214631 2.194967214 2.863365878 3.13858012 doxDHCer 18:0/23:0 2.753265997 1.440398678 2.113117271 1.80236967 2.044422798 2.057911758 2.323593636 1.193032276 1.00621156 1.080044057 1.43080267 0.817619145 0.694773102 0.620478767 0.866304196 0.834402775 doxDHCer 18:0/24:0 12.34633337 5.741742355 9.96096445 8.739150111 11.98457741 9.445427337 9.838208783 2.84953639 4.776297884 4.937903569 7.800661827 4.907988138 4.034601963 3.559831907 4.402780129 3.263630759 doxDHCer 18:0/24:1 2.626764268 1.600688066 2.008244043 2.988703555 2.357678793 2.822918375 2.839096099 1.935639367 1.62503538 2.222078357 2.110261392 1.426097526 1.140903279 0.799927262 1.25991469 1.115718983 Gluc/Gal-Cer 18:1/16:0 1159.223488 923.2901007 906.326148 831.5447864 929.3984611 1103.319107 1083.633094 807.9021189 1083.295263 1015.422682 1011.992747 806.2279367 1112.626322 701.3519479 704.4035218 939.8847944 Gluc/Gal-Cer 18:1/18:0 168.8375181 136.2501903 54.91644295 173.5393994 102.4174449 212.9107523 133.7033635 119.1266786 264.1393917 238.633917 198.5153451 140.8896149 176.9172942 170.4420368 181.5191898 116.5392676 Gluc/Gal-Cer 18:1/20:0 141.9726218 135.2904792 74.14207511 150.8051082 129.705517 201.415295 96.89979559 99.18807501 257.0715719 180.3209758 132.234321 155.3950584 123.1627204 122.6978641 141.3499028 108.564075 Gluc/Gal-Cer 18:1/22:0 1130.526895 717.1537453 241.8859596 996.7712281 399.0195607 1158.01555 736.4865176 514.9156006 1505.475254 1023.982795 834.5029282 622.69012 802.1567682 1047.053259 762.5017809 762.4784974 Gluc/Gal-Cer 18:1/24:0 1811.789815 1405.592933 362.0583534 1350.353909 576.815448 2028.253 1405.571449 428.4441158 2536.07303 1487.051711 1265.595408 852.1838192 1153.202744 1171.010531 843.1355461 1332.043379 Gluc/Gal-Cer 18:1/24:1 6421.826906 4448.021199 1377.359013 7237.8908 2732.523332 6896.510617 4260.968943 4903.308572 7217.9406 6111.679343 5661.576365 4672.280288 4923.937028 6448.674809 5474.286908 4201.725721 Lact-Cer 18:1/16:0 9.329529897 8.502788823 8.48597314 6.881125177 6.572238233 8.135564708 8.643220091 6.599778541 7.569019811 18.15620072 11.55558136 6.13015892 16.97187135 7.623632279 9.17602375 8.558679152 Lact-Cer 18:1/18:0 12.75597642 4.545081429 5.253033953 9.453208232 3.39773744 9.421778666 6.514563797 5.509058839 9.513007572 9.801315551 8.862653642 5.515525572 7.41371623 8.464967459 8.609814356 5.318275607 SO-C18:1 7505.721812 6621.409123 6653.569283 6316.589503 8810.337936 6423.504957 6695.264362 5641.34998 7816.706938 4982.430436 6291.913172 4140.521051 3842.186242 4214.618621 5449.28183 4288.690267 SA-C18:0 210.7878853 216.9164705 223.5487855 211.2625215 249.0419744 199.1898828 170.2712922 169.2595935 273.3954148 193.7816518 239.1912385 136.4950775 169.111691 191.7614901 215.5320756 178.7941871 doxSA-C18:0 32.22980059 24.86546184 27.19269341 24.83264952 40.57110393 27.58541757 31.06716136 29.45332766 11.03099961 12.3368978 15.13018614 12.59400933 6.917009151 9.696450747 13.28184852 7.846009669 SM-C14:0 686.9201739 671.7235239 622.5195521 450.2218465 723.6784974 626.913578 444.8210063 458.0154855 652.2254168 371.4339487 435.6902788 506.4598869 791.4632962 602.597478 675.0395919 493.6600814 SM-C16:0 8928.030699 9100.911572 8980.6223 7478.439192 8983.367001 9160.622586 8691.2272 8720.235144 9727.716741 9919.710413 9637.359114 8061.210251 10557.23048 7736.814728 7698.298039 8149.909433 SM-C18:0 1599.795762 1422.097313 1472.976906 1689.029287 1195.596742 1888.132299 1539.790778 1637.917971 2104.689896 2181.451902 2182.892698 1479.01352 2042.337701 1796.411109 1963.888202 1703.08908 SM-C18:1 205.420238 171.6766164 167.3745763 222.308401 131.9094321 210.4303225 203.9645479 214.1271094 264.856225 232.9790424 247.6618098 178.5781589 254.7914833 238.8636514 221.0773554 221.4080269 SM-C22:0 1919.604854 1744.483773 1327.122919 1543.570891 1173.604582 1710.264311 1734.03591 1370.943205 2276.13911 1896.961398 1762.404808 1311.115238 1929.82366 1675.571696 1603.930646 1608.804877 SM-C24:0 1852.933859 1397.50666 1219.588561 1389.986457 1098.337428 1842.925906 1697.000978 657.0773782 2511.702599 2101.922498 2035.178041 1199.22308 2125.868872 1619.448442 1312.77437 1643.721053 SM-C24:1 7130.705553 6278.999219 5471.078573 6591.939721 5451.804058 7340.993447 6189.363274 6631.717663 7485.72974 7722.587498 6439.194668 6352.671038 7437.161269 5805.558984 6087.054805 6344.241386 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name KEGG PubChem identifiers Cer 18:1/16:0 C00195 3495 Cer 18:1/18:0 C00195 3495 Cer 18:1/18:1 C00195 3495 Cer 18:1/20:0 C00195 3495 Cer 18:1/22:0 C00195 3495 Cer 18:1/23:0 C00195 3495 Cer 18:1/24:0 C00195 3495 DHCer 18:0/16:0 C12126 14273 DHCer 18:0/18:0 C12126 14273 DHCer 18:0/20:0 C12126 14273 DHCer 18:0/22:0 C12126 14273 DHCer 18:0/23:0 C12126 14273 DHCer 18:0/24:0 C12126 14273 DHCer 18:0/24:1 C12126 14273 doxCer 18:1/18:0 0 0 doxCer 18:1/20:0 0 0 doxCer 18:1/22:0 0 0 doxCer 18:1/22:1 0 0 doxCer 18:1/24:0 0 0 doxCer 18:1/24:1 0 0 doxDHCer 18:0/18:0 0 0 doxDHCer 18:0/20:0 0 0 doxDHCer 18:0/22:0 0 0 doxDHCer 18:0/23:0 0 0 doxDHCer 18:0/24:0 0 0 doxDHCer 18:0/24:1 0 0 Gluc/Gal-Cer 18:1/16:0 C01190 4416 Gluc/Gal-Cer 18:1/18:0 C01190 4416 Gluc/Gal-Cer 18:1/20:0 C01190 4416 Gluc/Gal-Cer 18:1/22:0 C01190 4416 Gluc/Gal-Cer 18:1/24:0 C01190 4416 Gluc/Gal-Cer 18:1/24:1 C01190 4416 Lact-Cer 18:1/16:0 C01290 4509 Lact-Cer 18:1/18:0 C01290 4509 SO-C18:1 C00319 3613 SA-C18:0 C00836 4094 doxSA-C18:0 0 0 SM-C14:0 C00550 3831 SM-C16:0 C00550 3831 SM-C18:0 C00550 3831 SM-C18:1 C00550 3831 SM-C22:0 C00550 3831 SM-C24:0 C00550 3831 SM-C24:1 C00550 3831 METABOLITES_END #END