#METABOLOMICS WORKBENCH michaelsa93_20170509_153519 DATATRACK_ID:902 STUDY_ID:ST000603 ANALYSIS_ID:AN000923 PROJECT_ID:PR000440 VERSION 1 CREATED_ON May 10, 2017, 1:52 pm #PROJECT PR:PROJECT_TITLE Urinary Volatile Compound, Associated with Chronic Inflammation In Interstitial PR:PROJECT_TITLE Cystitis PR:PROJECT_SUMMARY Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a clinical condition PR:PROJECT_SUMMARY that manifests as a sensory hypersensitivity of unknown cause and is PR:PROJECT_SUMMARY characterized by urinary frequency, bladder discomfort, and pelvic pain. In the PR:PROJECT_SUMMARY present volatolomic study, we have analyzed the VOCs unique to urine specimens PR:PROJECT_SUMMARY obtained from interstitial cystitis patients, in compassion to healthy PR:PROJECT_SUMMARY controls.This is the novel finding from comprehensive and unbiased metabolomics PR:PROJECT_SUMMARY analysis that urinary menthol is decreased in urine specimens from IC patients, PR:PROJECT_SUMMARY and that the reduced menthol level in IC is potentially linked to the chronic PR:PROJECT_SUMMARY inflammation, which is often observed in IC patients PR:INSTITUTE Cedars-Sinai Medical Center PR:LAST_NAME Kim PR:FIRST_NAME Jayoung PR:ADDRESS 8700 Beverly Blvd. Davis Research Building Ste 5071 Los Angeles, CA 90048 PR:EMAIL jayoung.kim@cshs.org PR:PHONE 310-423-7168 #STUDY ST:STUDY_TITLE Urinary Volatile Compound, Associated with Chronic Inflammation In Interstitial ST:STUDY_TITLE Cystitis ST:STUDY_SUMMARY Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a clinical condition ST:STUDY_SUMMARY that manifests as a sensory hypersensitivity of unknown cause and is ST:STUDY_SUMMARY characterized by urinary frequency, bladder discomfort, and pelvic pain. In the ST:STUDY_SUMMARY present volatolomic study, we have analyzed the VOCs unique to urine specimens ST:STUDY_SUMMARY obtained from interstitial cystitis patients, in compassion to healthy ST:STUDY_SUMMARY controls.This is the novel finding from comprehensive and unbiased metabolomics ST:STUDY_SUMMARY analysis that urinary menthol is decreased in urine specimens from IC patients, ST:STUDY_SUMMARY and that the reduced menthol level in IC is potentially linked to the chronic ST:STUDY_SUMMARY inflammation, which is often observed in IC patients 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 Health Sciences Drive, Davis, California, 95616, USA ST:EMAIL ofiehn@ucdavis.edu ST:PHONE (530) 754-8258 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS C10_001 160427blvsa17_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C13_002 160427blvsa10_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C15_003 160427blvsa09_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C16_004 160427blvsa08_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C17_005 160427blvsa19_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C18_006 160427blvsa15_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C26_007 160427blvsa14_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C27_008 160427blvsa05_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C28_009 160427blvsa18_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS C33_010 160427blvsa13_1 Treatment:control Source=Urine SUBJECT_SAMPLE_FACTORS IC12_013 160427blvsa01_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC14_014 160427blvsa20_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC19_015 160427blvsa12_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC20_016 160427blvsa02_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC22_017 160427blvsa04_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC30_018 160427blvsa11_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC31_019 160427blvsa07_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC43_020 160427blvsa03_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC5_011 160427blvsa16_1 Treatment:IC Source=Urine SUBJECT_SAMPLE_FACTORS IC9_012 160427blvsa06_1 Treatment:IC Source=Urine #COLLECTION CO:COLLECTION_SUMMARY First morning urine specimens were obtained using clean catch methods, and sent CO:COLLECTION_SUMMARY to clinical laboratory. After a 10 min centrifugation to remove cell debris, CO:COLLECTION_SUMMARY urine specimens were stored at −80◦C until further analysis. #TREATMENT TR:TREATMENT_SUMMARY No treatment #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 1. Vortex the urine samples for about 10s to obtain a homogenized sample using SP:SAMPLEPREP_SUMMARY the MiniVortexer VWR. 2. Aliquot 15-30ul and add 1ml extraction solution. The SP:SAMPLEPREP_SUMMARY extraction solution has to be pre-chilled using the ThermoElectron Neslab RTE SP:SAMPLEPREP_SUMMARY 740 cooling bath set to -20°C. 3. Vortex the sample for about 10s and shake for SP:SAMPLEPREP_SUMMARY 5min at 4°C using the Orbital Mixing Chilling/Heating plate. If you are using SP:SAMPLEPREP_SUMMARY more than one sample, keep the rest of the samples on ice (chilled at <0°C with SP:SAMPLEPREP_SUMMARY NaCl). 4. Centrifuge samples for 2min at 14000 rcf using the centrifuge SP:SAMPLEPREP_SUMMARY Eppendorf 5415 D. 5. Aliquot 2X 0.5ml supernatant. One for analysis and one for SP:SAMPLEPREP_SUMMARY backup. Store 2nd aliquot in -20°C freezer. 6. Evaporate 0.5ml aliquots of the SP:SAMPLEPREP_SUMMARY sample in the Labconco Centrivap cold trap concentrator to complete dryness. 7. SP:SAMPLEPREP_SUMMARY Submit to derivatization. SP:SAMPLEPREP_PROTOCOL_FILENAME SOP_Extraction_of_Urine.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um) CH:COLUMN_NAME 0.25 μm film made of 95% dimethyl/5%diphenylpolysiloxane) CH:FLOW_RATE 1 ml/min CH:COLUMN_TEMPERATURE 50 - 330°C CH:COLUMN_PRESSURE 7.7 PSI (initial condition) CH:INJECTION_TEMPERATURE 50°C ramped to 250°C by 12°C/s CH:SAMPLE_INJECTION 0.5µl CH:OVEN_TEMPERATURE 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min CH:TRANSFERLINE_TEMPERATURE 230°C CH:WASHING_BUFFER Ethyl Acetate CH:SAMPLE_LOOP_SIZE 30 m length x 0.25 mm internal diameter CH:RANDOMIZATION_ORDER Excel generated #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Varian 210-MS GC Ion Trap MS:INSTRUMENT_TYPE GC Ion Trap MS:MS_TYPE EI MS:ION_MODE POSITIVE MS:ION_SOURCE_TEMPERATURE 250°C MS:IONIZATION_ENERGY 70eV MS:MASS_ACCURACY Nominal MS:SOURCE_TEMPERATURE 250°C MS:SCANNING_CYCLE 17 Hz MS:SCANNING_RANGE 85-500 MS:SKIMMER_VOLTAGE 1850 V #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Counts MS_METABOLITE_DATA_START Samples 160427blvsa17_1 160427blvsa10_1 160427blvsa09_1 160427blvsa08_1 160427blvsa19_1 160427blvsa15_1 160427blvsa14_1 160427blvsa05_1 160427blvsa18_1 160427blvsa13_1 160427blvsa01_1 160427blvsa20_1 160427blvsa12_1 160427blvsa02_1 160427blvsa04_1 160427blvsa11_1 160427blvsa07_1 160427blvsa03_1 160427blvsa16_1 160427blvsa06_1 Factors Treatment:control Treatment:control Treatment:control Treatment:control Treatment:control Treatment:control Treatment:control Treatment:control Treatment:control Treatment:control Treatment:IC Treatment:IC Treatment:IC Treatment:IC Treatment:IC Treatment:IC Treatment:IC Treatment:IC Treatment:IC Treatment:IC 2-Heptanone, 4,6-dimethyl- 10861 7432 5502 6840 5128 4226 2158 7012 1970 4502 1878 8494 8236 5210 2339 2734 7868 8040 6328 9536 2-Heptanone, 4-methyl- 21740 16862 10920 13605 9814 7831 3308 16918 3006 8439 4078 21001 19064 9155 6732 1920 19844 15833 14307 21256 2-Heptanone 2499 3935 2817 2610 2188 7432 5034 4263 3753 4614 2139 2873 1668 1254 5474 1772 2325 2153 9130 4145 4-Heptanone 22915 97506 25148 55730 76229 194896 227266 75812 109550 30610 270328 32209 64385 24148 97657 43861 21656 108689 51015 28037 Benzaldehyde, 4-methyl- 7241 4509 6192 12714 3429 5000 1937 4685 3044 8964 1538 4321 3985 6255 1567 1461 4092 3869 3941 5290 Benzaldehyde 2708 980 775 13614 989 1204 4955 72550 395 1315 678 1287 4258 860 2094 752 2208 1724 2387 9863 Benzene, 1,3-bis(1,1-dimethylethyl)- 5752 6890 4977 11361 5647 4020 2890 6351 2165 5613 2039 7510 4888 5988 1775 934 54663 6986 5604 6729 Benzoic acid, 2-[(trimethylsilyl)oxy]-, trimethylsilyl ester 1728 903 540 905 2353 612 543 1401 446 1354 363 1938 780 728 877 242 1206 1987 2509 2173 Ethylbenzene 5469 7338 7928 9139 9591 1951 3913 8232 2683 5854 2694 37113 4031 2464 1995 1008 19764 7003 6735 7095 Hexaethylene glycol dimethyl ether 3959 2718 1462 2390 3287 1696 1424 2035 745 3435 758 3763 2267 2011 1173 556 3147 4114 3049 3498 o-Xylene 5469 7338 7928 9139 9591 1951 3913 8232 2683 5854 2694 37113 4031 2464 1995 1008 19764 7003 6735 7095 styrene 5694 5952 6046 9125 5211 3857 2148 3883 1701 11155 2482 7158 5587 2720 2525 2762 12263 7661 5683 8493 t-Butyl ethyl ether2 19150 16797 21771 31084 14606 6027 12141 4844 15827 2718 12724 17674 10631 3646 1921 7068 6335 10015 13762 Thiocyanic acid, 2-propenyl ester 1497 7474 833 2829 2916 3464 1262 1644 500 3641 604 938 853 2502 1118 438 1501 2719 3525 toluene 14670 9597 8101 16070 10241 4590 8416 2275 11930 2625 11644 7317 10860 5870 2138 21443 13956 8567 15523 2-Pentanone 22291 54326 9230 26189 26576 27101 10988 148235 109629 8343 41454 27360 9284 20193 15496 14910 27096 18913 2-Propanol, 2-methyl- 10570 11793 14042 21161 4829 2757 4943 16289 2002 8254 15429 9159 2863 3264 7357 7740 8137 Allyl Isothiocyanate 2904 96579 922 38086 2874 12804 14705 1222 41249 1665 6807 29864 13503 1342 1864 35167 42954 Cyclohexanol, 5-methyl-2-(1-methylethyl)-, (1à,2á,5à)-(ñ)- 631 4233 2410 3701 550 3309 3008 1374 1344 751 487 1934 465 363 1980 672 734 3069 664 Hexane 29240 22285 13531 21648 29652 11431 11420 18595 5738 24555 6243 28767 18169 15314 9401 4209 27628 27939 35528 Phenol, 2,4-bis(1,1-dimethylethyl)- 114302 27501 79083 46418 4244 2351 2159 56210 9444 2498 5471 60716 2884 4095 1807 339 4151 44321 65989 Phenol 2159 12587 971 2087 2356 805 1813 1873 1105 1145 2692 3469 2494 3406 Propylamine 10570 11793 14042 21161 4829 2757 4943 16289 2002 8254 15429 9159 2863 3264 7357 7740 8137 Pyrrole 3077 21755 1389 8889 3546 3295 3162 1552 2576 10147 7493 5972 1431 2415 9118 2841 2998 4-pentenal, 2-methyl 7250 4696 3604 5428 5415 2484 4267 1593 1636 7198 2654 982 7371 23720 5493 8481 Benzaldehyde, 3,5-dimethyl- 572 2478 115570 32812 35564 4001 149 3156 2861 108044 217998 60008 90361 115872 2285 2102 Benzene, (1-methylethyl)- 4359 3214 1958 3525 3574 1754 1565 3959 716 3876 1049 4502 2466 2248 4844 5711 3826 5167 Acetophenone 3181 1604 1033 912 444 1956 411 1869 1808 984 652 12370 422 Methyl Isobutyl Ketone 5892 7377 4104 5570 4285 3209 3157 4942 907 8840 1853 7068 5401 2098 2868 5013 6861 1-Hexanol, 2-ethyl- 4607 2308 1913 1535 1013 1036 4082 11321 3103 1615 832 124913 2668 2351 2-Cyclohexen-1-one, 2-methyl-5-(1-methylethenyl)-, (S)- 12738 1219 3192 14404 2097 8130 7067 2488 3659 44750 504 8866 51148 Benzene, (1-methyl-1-butenyl)- 1778 3005 565 1852 1609 2147 1686 1383 1318 865 504 829 1788 1445 Benzene, (2-isothiocyanatoethyl)- 16012 6029 5278 1786 533 1920 782 1782 783 1055 2461 7684 18438 benzoylformic acid 500 652 676 1143 1129 1537 358 374 1258 1614 Benzene, chloro- 1091 2290 3426 1229 1716 5848 549 1476 3395 907 485 4727 Cyclohexanone 539 232 2010 3530 39025 1142 Cyclopropane, isothiocyanato- 2420 1914 974 792 392 1166 1921 2-Cyclohexen-1-one, 3-methyl-6-(1-methylethyl)- 1193 1560 1715 2792 570 50578 4395 1391 7039 2-Propenoic acid, 2-methyl-, 1,2-ethanediyl ester 1968 16093 2005 4-Carene, (1S,3R,6R)-(-)- 604 728 1330 2726 874 1361 Amylene Hydrate 1713 1119 1956 337 1185 Benzaldehyde, 2,5-dimethyl- 1917 549 1121 1-Octanol 414 714 2,4,6-Octatrienal 737 2246 385 2-Cyclohexen-1-one, 3,5,5-trimethyl- 1584 54906 5-Methyl-1-heptanol 352 242 180 911 Propofol 897 46898 52658 9366 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name m/z 2-Heptanone, 4,6-dimethyl- 423.714 2-Heptanone, 4-methyl- 396.607 2-Heptanone 370.794 4-Heptanone 360.151 Benzaldehyde, 4-methyl- 478.457 Benzaldehyde 414.835 Benzene, 1,3-bis(1,1-dimethylethyl)- 550.546 Benzoic acid, 2-[(trimethylsilyl)oxy]-, trimethylsilyl ester 588.472 Ethylbenzene 361.151 Hexaethylene glycol dimethyl ether 648.859 o-Xylene 361.092 styrene 373.146 t-Butyl ethyl ether2 228.028 Thiocyanic acid, 2-propenyl ester 362.033 toluene 301.939 2-Pentanone 259.78 2-Propanol, 2-methyl- 201.097 Allyl Isothiocyanate 366.56 Cyclohexanol, 5-methyl-2-(1-methylethyl)-, (1à,2á,5à)-(ñ)- 520.734 Hexane 316.933 Phenol, 2,4-bis(1,1-dimethylethyl)- 652.799 Phenol 417.658 Propylamine 200.803 Pyrrole 292.414 4-pentenal, 2-methyl 321.108 Benzaldehyde, 3,5-dimethyl- 540.902 Benzene, (1-methylethyl)- 429.182 Acetophenone 469.284 Methyl Isobutyl Ketone 287.239 1-Hexanol, 2-ethyl- 443.353 2-Cyclohexen-1-one, 2-methyl-5-(1-methylethenyl)-, (S)- 551.78 Benzene, (1-methyl-1-butenyl)- 527.026 Benzene, (2-isothiocyanatoethyl)- 643.92 benzoylformic acid 481.75 Benzene, chloro- 348.215 Cyclohexanone 378.497 Cyclopropane, isothiocyanato- 357.329 2-Cyclohexen-1-one, 3-methyl-6-(1-methylethyl)- 557.19 2-Propenoic acid, 2-methyl-, 1,2-ethanediyl ester 573.713 4-Carene, (1S,3R,6R)-(-)- 461.522 Amylene Hydrate 240.258 Benzaldehyde, 2,5-dimethyl- 536.375 1-Octanol 465.168 2,4,6-Octatrienal 421.715 2-Cyclohexen-1-one, 3,5,5-trimethyl- 496.214 5-Methyl-1-heptanol 451.232 Propofol 596.174 METABOLITES_END #END