#METABOLOMICS WORKBENCH michaelsa93_20151201_9336041_mwtab.txt DATATRACK_ID:444 efahy_20160115_125346 STUDY_ID:ST000332 ANALYSIS_ID:AN000532 PROJECT_ID:PR000266 VERSION 1 CREATED_ON January 15, 2016, 12:53 pm #PROJECT PR:PROJECT_TITLE Effects of Giardia intestinalis on GI tract PR:PROJECT_SUMMARY This experiment aimed to see the effects of Giardia Intestinalis on the small PR:PROJECT_SUMMARY intestine of mice. The metabolites of the proximal and distal ends of the small PR:PROJECT_SUMMARY intestine of healthy mice were compared to those of mice who had been infected PR:PROJECT_SUMMARY with Giardia intestinalis for 7 days. PR:INSTITUTE University of California, Davis PR:DEPARTMENT Genome and Biomedical Sciences Facility PR:LABORATORY WCMC Metabolomics Core PR:LAST_NAME Fiehn PR:FIRST_NAME Oliver PR:ADDRESS 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, PR:ADDRESS CA 95616 PR:EMAIL ofiehn@ucdavis.edu PR:PHONE (530) 754-8258 PR:FUNDING_SOURCE U24DK097154 #STUDY ST:STUDY_TITLE Effects of Giardia intestinalis on mice GI tract ST:STUDY_SUMMARY This experiment aimed to see the effects of Giardia Intestinalis on the small ST:STUDY_SUMMARY intestine of mice. The metabolites of the proximal and distal ends of the small ST:STUDY_SUMMARY intestine of healthy mice were compared to those of mice who had been infected ST:STUDY_SUMMARY with Giardia intestinalis for 7 days. ST:INSTITUTE University of California, Davis ST:DEPARTMENT Genome and Biomedical Sciences Facility ST:LABORATORY WCMC Metabolomics Core ST:LAST_NAME Fiehn ST:FIRST_NAME Oliver ST:ADDRESS 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, ST:ADDRESS CA 95616 ST:EMAIL ofiehn@ucdavis.edu ST:PHONE (530) 754-8258 ST:NUM_GROUPS 8 ST:TOTAL_SUBJECTS 28 #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Mus musculus #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 1.prox.56 Location:uninfected proximal SUBJECT_SAMPLE_FACTORS - 2.prox.56 Location:uninfected proximal SUBJECT_SAMPLE_FACTORS - 3.prox.56 Location:uninfected proximal SUBJECT_SAMPLE_FACTORS - 5.prox.56 Location:infected proximal SUBJECT_SAMPLE_FACTORS - 6.prox.56 Location:infected proximal SUBJECT_SAMPLE_FACTORS - 7.prox.56 Location:infected proximal SUBJECT_SAMPLE_FACTORS - 8.prox.56 Location:infected proximal SUBJECT_SAMPLE_FACTORS - 1.dist.56 Location:uninfected distal SUBJECT_SAMPLE_FACTORS - 2.dist.56 Location:uninfected distal SUBJECT_SAMPLE_FACTORS - 3.dist.56 Location:uninfected distal SUBJECT_SAMPLE_FACTORS - 5.dist.56 Location:infected distal SUBJECT_SAMPLE_FACTORS - 6.dist.56 Location:infected distal SUBJECT_SAMPLE_FACTORS - 7.dist.56 Location:infected distal SUBJECT_SAMPLE_FACTORS - 8.dist.56 Location:infected distal #COLLECTION CO:COLLECTION_SUMMARY C57B6J mice were infected via oral gavage with Giardia intestinalis, then CO:COLLECTION_SUMMARY sacrificed 7 days later. Intestinal samples containing Giardia were excised and CO:COLLECTION_SUMMARY flash frozen in liquid nitrogen. CO:COLLECTION_PROTOCOL_FILENAME StudyDesign-JohnPham-12814.pdf CO:SAMPLE_TYPE Small intestine tissue #TREATMENT TR:TREATMENT_SUMMARY 3 segments originating from the proximal small intestine of uninfected mice 3 TR:TREATMENT_SUMMARY segments originating from the distal small intestine of uninfected mice 4 TR:TREATMENT_SUMMARY segments originating from the proximal small intestine of Giardiainfected mice TR:TREATMENT_SUMMARY 4 segments originating from the distal small intestine of Giardiainfected mice TR:TREATMENT_PROTOCOL_FILENAME StudyDesign-JohnPham-12814.pdf #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 1. Weigh 50 mg tissue sample in to a 25 ml conical polypropylene centrifuge SP:SAMPLEPREP_SUMMARY tube. 2. Add 2.5mL extraction solvent to the tissue sample and homogenize for 45 SP:SAMPLEPREP_SUMMARY seconds ensuring that sample resembles a powder. In between samples, clean the SP:SAMPLEPREP_SUMMARY homogenizer in solutions of methanol, acetone, water, and the extraction SP:SAMPLEPREP_SUMMARY solvent. 3. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X SP:SAMPLEPREP_SUMMARY 500µl supernatant, one for analysis and one for a backup sample. Store backup SP:SAMPLEPREP_SUMMARY aliquot in the -20°C freezer. 4. Evaporate one 500µl aliquot of the sample in SP:SAMPLEPREP_SUMMARY the Labconco Centrivap cold trap concentrator to complete dryness 5. The dried SP:SAMPLEPREP_SUMMARY aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 6. SP:SAMPLEPREP_SUMMARY Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 7. Remove SP:SAMPLEPREP_SUMMARY supernatant to a new Eppendorff tube. 8. Evaporate the supernatant to dryness in SP:SAMPLEPREP_SUMMARY the the Labconco Centrivap cold trap concentrator. 9. Submit to derivatization. SP:SAMPLEPREP_PROTOCOL_FILENAME SOP Extraction of Mammalian Tissue Samples.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY UPLC CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Unspecified CH:COLUMN_NAME Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) CH:COLUMN_NAME 1.7um Pre-Column CH:FLOW_GRADIENT 15% B to 99% B CH:FLOW_RATE 0.6 mL/min CH:COLUMN_TEMPERATURE 65 C CH:METHODS_FILENAME Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf CH:SOLVENT_A 60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid CH:SOLVENT_B 9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid CH:COLUMN_PRESSURE 450-850 bar CH:INTERNAL_STANDARD See data dictionary CH:RETENTION_TIME See data dictionary CH:SAMPLE_INJECTION 1.67 uL CH:ANALYTICAL_TIME 13 min CH:CAPILLARY_VOLTAGE 3500 CH:TIME_PROGRAM 15 min CH:WEAK_WASH_SOLVENT_NAME Isopropanol CH:WEAK_WASH_VOLUME 5 seconds CH:STRONG_WASH_SOLVENT_NAME Isopropanol CH:TARGET_SAMPLE_TEMPERATURE Autosampler temp 4 C CH:RANDOMIZATION_ORDER Excel #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME WCMC Metabolomics Core AN:DETECTOR_TYPE TOF MCP AN:SOFTWARE_VERSION MassHunter AN:DATA_FORMAT .d #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6550 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:CAPILLARY_VOLTAGE 3500 MS:COLLISION_GAS Nitrogen MS:DRY_GAS_FLOW 8 l/min MS:DRY_GAS_TEMP 325 MS:FRAGMENT_VOLTAGE 120 MS:FRAGMENTATION_METHOD Auto MS/MS MS:ION_SOURCE_TEMPERATURE 325 MS:ION_SPRAY_VOLTAGE 1000 MS:IONIZATION Pos MS:PRECURSOR_TYPE Intact Molecule MS:REAGENT_GAS Nitrogen MS:SOURCE_TEMPERATURE 325 C MS:DESOLVATION_GAS_FLOW 11 l/min MS:DESOLVATION_TEMPERATURE 350 C MS:NEBULIZER 35 psig MS:OCTPOLE_VOLTAGE 750 MS:RESOLUTION_SETTING Extended Dynamic Range MS:SCAN_RANGE_MOVERZ 60-1700 Da MS:SCANNING_CYCLE 2 Hz MS:SCANNING_RANGE 60-1700 Da MS:SKIMMER_VOLTAGE 65 #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Peak height MS_METABOLITE_DATA_START Samples 1.prox.56 2.prox.56 3.prox.56 5.prox.56 6.prox.56 7.prox.56 8.prox.56 1.dist.56 2.dist.56 3.dist.56 5.dist.56 6.dist.56 7.dist.56 8.dist.56 Factors Location:uninfected proximal Location:uninfected proximal Location:uninfected proximal Location:infected proximal Location:infected proximal Location:infected proximal Location:infected proximal Location:uninfected distal Location:uninfected distal Location:uninfected distal Location:infected distal Location:infected distal Location:infected distal Location:infected distal Ceramide (d33:1) 28886 24510 29938 22228 30164 34776 14736 9121 10153 10570 28039 Ceramide (d34:0) 39358 26596 36955 30878 42498 21471 29834 38227 29239 30411 44897 32557 40122 30547 Ceramide (d34:1) 639411 444694 593799 347224 698211 188583 530719 441977 293404 286320 475452 386643 620034 331135 Ceramide (d38:1) 13772 10392 14346 21292 14149 10150 15662 10309 Ceramide (d40:1) 22035 17853 21438 15006 30140 25133 13505 11792 21469 16338 25752 12725 Ceramide (d41:1) 14135 11173 11312 10188 16131 15097 9132 14238 Ceramide (d42:1) 38436 29551 32216 16212 45065 37484 15286 16529 11232 47832 33199 39868 18347 Ceramide (d42:2) 45733 30418 37242 16775 62857 48706 29913 22141 15812 51438 48420 52526 36805 FA (18:1) (oleic acid) 790668 186396 363462 1041863 615802 1546829 496989 276288 502478 554153 1479486 555609 1082203 952012 FA (20:1) (eicosenoic acid) 36428 10318 18649 61427 30057 94070 33214 11841 16605 29642 64688 27877 56598 84793 FA (20:3) (homo-gamma-linolenic acid) 22070 8054 9589 16409 36126 345269 23843 17999 35319 39992 43564 97430 50617 75423 FA (20:4) (arachidonic acid) 240587 98547 83090 121885 239935 1369113 224179 66003 205135 233909 147786 351417 428268 398171 FA (20:5) (eicosapentaenoic acid) 32922 14973 10553 26720 23767 130450 22723 12257 25556 24649 27087 32161 37482 44629 FA (22:6) (docosahexaenoic acid) 160986 66115 70569 96496 130361 621223 115215 34846 114485 145291 139023 174988 195948 183547 FA (24:0) (lignoceric acid) 6118 3906 4996 6891 7392 36670 5244 9192 12940 12605 11512 11224 9165 38796 GlcCer(d14:1(4E)/20:0(2OH)) 27504 27436 22869 19559 18769 18953 7848 16877 LPC (16:0) 41677 35875 29511 34298 31794 51663 39078 24532 79385 146817 38456 32923 42370 93351 LPC (18:0) 50896 44611 38583 42519 44101 37981 53821 31624 56388 78747 49929 48620 55941 72569 PC (34:1) 41574 37076 34758 36121 38663 21253 37773 27267 37978 33948 57634 48004 42142 35257 PC (34:2) 271661 282711 209781 241226 185069 31671 226739 55071 96205 71989 116853 134861 191863 60203 PC (36:1) 41024 44122 38592 35830 38100 13526 37906 25096 29421 24642 48561 35692 37436 26247 PC (36:2) 265912 292224 232611 249573 207329 29946 259330 61918 81929 58400 121530 138108 195475 63453 PC (36:3) 42028 43576 33541 43301 34673 38601 25904 30008 23424 42908 39003 31061 25624 PC (36:4) 62932 60802 56072 45729 57142 21610 58507 25736 50763 43614 42703 55980 65398 33170 PC (36:5) 19067 19357 15691 16777 14273 14626 12721 12274 13800 13996 PC (38:3) 10683 9184 9842 10560 10455 13637 12838 8812 PC (38:4) 52843 53653 49258 37937 49973 13601 54685 20002 30028 22734 31096 43195 51740 23228 PC (38:5) 10700 11815 9305 10032 9160 7589 8545 8830 PC (38:6) 29656 27942 21863 18212 23712 25962 16950 15829 21603 22872 23641 PC (40:6) 19340 21839 19064 15940 19701 21549 9015 14063 10352 16075 17149 19762 10108 PE (34:1) 47614 61629 41575 56689 44183 46980 12527 22305 10953 60017 48965 41387 17332 PE (34:2) 125294 148022 96915 133468 80051 101588 12819 16660 10913 39414 39427 70866 13613 PE (36:2) 576256 636041 550954 584680 483417 42893 532370 105992 122428 76291 289978 324471 430066 104416 PE (36:3) 56946 66983 46476 69524 47199 51615 23076 22258 17428 50906 41306 39396 21617 PE (36:4) 363764 398626 341064 330403 311423 338822 23624 61930 29388 113095 145316 297297 31422 PE (38:4) 725063 747483 690324 652429 668372 68296 726085 215647 327793 169464 454215 560459 657602 247970 PE (38:6) 145466 128165 105732 76145 107772 15731 115100 22506 41134 20472 65112 98458 111865 25526 PE (p-36:4) or PE (o-36:5) 25717 25244 25293 18064 33092 28023 10019 16010 10214 23946 34419 31182 12535 PE (p-38:3) or PE (o-38:4) 38724 31285 32967 26711 29735 30041 13218 16882 10469 20168 29003 32553 12642 PE (p-38:4) or PE (o-38:5) 44754 44737 52160 13912 56445 14646 24931 15400 30284 40191 50516 20557 PE (p-38:5) or PE (o-38:6) 10928 10210 9871 13503 11213 11980 14065 13502 PE (p-40:4) or PE (o-40:5) 10102 11598 9373 8559 10289 14013 10926 PE (p-40:5) or PE (o-40:6) 46940 38501 39297 32309 36425 11288 37219 16493 23102 13037 27824 40745 40106 14906 PE (p-40:6) or PE (o-40:7) 47479 53046 41766 34496 46934 11245 56662 10984 18910 10014 30205 39201 46486 15127 SM (d34:1) 96008 106693 94869 89400 94497 50441 103262 42776 55588 38625 81282 73184 98502 50973 SM (d36:1) 8290 9264 9072 9901 9633 SM (d40:1) 12156 12105 11907 13632 12161 9760 13828 13746 13006 SM (d42:1) 10783 10154 12616 11149 13544 12803 12587 SM (d42:2) 15773 15155 16168 11513 20017 11652 18445 9339 15247 21372 22127 20297 13131 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Identifier m/z RT Adducts Ceramide (d33:1) 5.56_558.47 558.4651 5.559 [M+Cl]- Ceramide (d34:0) 6.15_598.54_6.16_574.50 598.5356_574.4960 6.153 [M+HAc-H]-_[M+Cl]- Ceramide (d34:1) 5.96_572.48_5.98_596.53 572.4825_596.5263 5.97 [M+Cl]-_[M+HAc-H]- Ceramide (d38:1) 7.31_628.54 628.5436 7.314 [M+Cl]- Ceramide (d40:1) 8.00_656.57 656.5748 8.002 [M+Cl]- Ceramide (d41:1) 8.34_670.59 670.5904 8.338 [M+Cl]- Ceramide (d42:1) 8.63_708.65_8.64_684.61 708.6501_684.6059 8.6355 [M+HAc-H]-_[M+Cl]- Ceramide (d42:2) 7.97_682.59_7.97_706.63 682.5928_706.6340 7.9665 [M+Cl]- _[M+HAc-H]- FA (18:1) (oleic acid) 2.82_281.25 281.2487 2.816 [M-H]- FA (20:1) (eicosenoic acid) 3.40_309.28 309.2797 3.399 [M-H]- FA (20:3) (homo-gamma-linolenic acid) 2.48_305.25 305.249 2.481 [M-H]- FA (20:4) (arachidonic acid) 2.03_303.23 303.233 2.032 [M-H]- FA (20:5) (eicosapentaenoic acid) 1.59_301.22 301.2173 1.591 [M-H]- FA (22:6) (docosahexaenoic acid) 1.81_327.23 327.2329 1.814 [M-H]- FA (24:0) (lignoceric acid) 5.37_367.36 367.3576 5.371 [M-H]- GlcCer(d14:1(4E)/20:0(2OH)) 5.08_774.57 774.5725 5.079 [M+HAc-H]- LPC (16:0) 1.65_554.35 554.3458 1.654 [M+HAc-H]- LPC (18:0) 2.47_582.38 582.3772 2.468 [M+HAc-H]- PC (34:1) 5.81_818.59 818.5909 5.815 [M+HAc-H]- PC (34:2) 5.31_816.58 816.5755 5.311 [M+HAc-H]- PC (36:1) 6.50_846.62 846.6226 6.499 [M+HAc-H]- PC (36:2) 5.98_844.61 844.6065 5.975 [M+HAc-H]- PC (36:3) 5.40_842.59 842.5907 5.398 [M+HAc-H]- PC (36:4) 5.21_840.58 840.5753 5.205 [M+HAc-H]- PC (36:5) 4.80_838.56 838.5596 4.796 [M+HAc-H]- PC (38:3) 6.16_870.62 870.6223 6.159 [M+HAc-H]- PC (38:4) 5.88_868.61 868.6068 5.877 [M+HAc-H]- PC (38:5) 5.39_866.59 866.5908 5.393 [M+HAc-H]- PC (38:6) 5.05_864.58 864.5754 5.05 [M+HAc-H]- PC (40:6) 5.69_892.61 892.6066 5.685 [M+HAc-H]- PE (34:1) 5.96_716.52 716.523 5.958 [M-H]- PE (34:2) 5.44_714.51 714.5066 5.439 [M-H]- PE (36:2) 6.12_742.54 742.5388 6.122 [M-H]- PE (36:3) 5.51_740.52 740.5228 5.51 [M-H]- PE (36:4) 5.33_738.51 738.5076 5.332 [M-H]- PE (38:4) 6.00_766.54 766.5391 6.002 [M-H]- PE (38:6) 5.18_762.51 762.5077 5.184 [M-H]- PE (p-36:4) or PE (o-36:5) 5.63_722.51 722.5123 5.63 [M-H]- PE (p-38:3) or PE (o-38:4) 6.44_752.56 752.5592 6.444 [M-H]- PE (p-38:4) or PE (o-38:5) 6.33_750.54 750.5439 6.33 [M-H]- PE (p-38:5) or PE (o-38:6) 5.68_748.53 748.5282 5.678 [M-H]- PE (p-40:4) or PE (o-40:5) 7.00_778.58 778.577 7.002 [M-H]- PE (p-40:5) or PE (o-40:6) 6.24_776.56 776.5594 6.24 [M-H]- PE (p-40:6) or PE (o-40:7) 6.12_774.54 774.5436 6.119 [M-H]- SM (d34:1) 4.99_761.58 761.58 4.992 [M+HAc-H]- SM (d36:1) 5.69_789.61 789.6114 5.689 [M+HAc-H]- SM (d40:1) 7.10_845.67 845.6741 7.1 [M+HAc-H]- SM (d42:1) 7.76_873.71 873.7057 7.765 [M+HAc-H]- SM (d42:2) 7.06_871.69 871.6902 7.055 [M+HAc-H]- METABOLITES_END #END