#METABOLOMICS WORKBENCH Arun_Sreekumar_20170519_140734 DATATRACK_ID:916 STUDY_ID:ST000615 ANALYSIS_ID:AN000944 PROJECT_ID:PR000447 VERSION 1 CREATED_ON June 1, 2017, 1:06 pm #PROJECT PR:PROJECT_TITLE sacosine levels in prostate cancer disparity PR:PROJECT_SUMMARY GC/MS measurement of sarcosine levels in urine samples from prostate cancer and PR:PROJECT_SUMMARY case control patients in a group of ancestry verified African American and PR:PROJECT_SUMMARY European Americans. PR:INSTITUTE Baylor College of Medicine PR:LAST_NAME Sreekumar PR:FIRST_NAME Arun PR:ADDRESS One Baylor Plaza, Houston, TX, 77030, USA PR:EMAIL Arun.Sreekumar@bcm.edu PR:PHONE 713-798-3305 #STUDY ST:STUDY_TITLE GC/MS measurement of sarcosine in urine samples ST:STUDY_SUMMARY GC/MS measurement of sarcosine in urine samples from prostate cancer and case ST:STUDY_SUMMARY control patients in a group of ancestry verified African American and European ST:STUDY_SUMMARY Americans. ST:INSTITUTE Baylor College of Medicine ST:LAST_NAME Sreekumar ST:FIRST_NAME Arun ST:ADDRESS One Baylor Plaza, Houston, TX, 77030, USA ST:EMAIL Arun.Sreekumar@bcm.edu ST:PHONE 713-798-3305 #SUBJECT SU:SUBJECT_TYPE Humans SU:SUBJECT_SPECIES Homo sapiens #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 15298 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 15862 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 16710 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 17024 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 17122 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 17234 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 17585 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 17587 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 17721 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 17817 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 17848 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 17879 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 17891 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 17893 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 17897 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 17902 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 17962 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 17985 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18004 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18010 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18013 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18014 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18018 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18020 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18030 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18035 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18054 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18056 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18061 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18062 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18063 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18064 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18072 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18073 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18077 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18083 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18091 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18097 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18098 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18102 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18106 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18112 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18137 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18140 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18154 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18156 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18162 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18174 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18175 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18225 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18240 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18250 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18261 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18262 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18265 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18277 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18317 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18331 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18415 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18469 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18489 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18542 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18613 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18661 Diagnosis:Case control | RACE:- SUBJECT_SAMPLE_FACTORS - 18734 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18742 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18830 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18850 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18882 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18887 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18901 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 18918 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 18998 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 19034 Diagnosis:Prostate cancer | RACE:Caucasian SUBJECT_SAMPLE_FACTORS - 19049 Diagnosis:Prostate cancer | RACE:African American SUBJECT_SAMPLE_FACTORS - 19169 Diagnosis:Prostate cancer | RACE:Caucasian #COLLECTION CO:COLLECTION_SUMMARY Urine from ancestry typed AA and EA prostate cancer patients were used for this CO:COLLECTION_SUMMARY analysis. Urine specimens were spun and the supernatant was stored at −70°C CO:COLLECTION_SUMMARY until analysis. #TREATMENT TR:TREATMENT_SUMMARY NA #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Urine supernatants were diluted with methanol containing spiked labeled internal SP:SAMPLEPREP_SUMMARY standards (d3-sarcosine and d3-alanine), and extracted overnight at 4°C, using SP:SAMPLEPREP_SUMMARY 1:1 molar ratio of water/chloroform at room temperature, with constant shaking. SP:SAMPLEPREP_SUMMARY The aqueous methanolic layer was recovered, dried and azeotroped twice by adding SP:SAMPLEPREP_SUMMARY 100 mL dimethylformamide (DMF), mixed and dried using a speedvac for 30 minutes. SP:SAMPLEPREP_SUMMARY Following this, 100 mL of DMF and SP:SAMPLEPREP_SUMMARY N-methyl-N-tert-butylmethylsilyltrifluoroacetamide (MtBSTFA) + 1% SP:SAMPLEPREP_SUMMARY t-butyl-dimethylchlorosilane were added and incubated at 60°C for 1 hr. The SP:SAMPLEPREP_SUMMARY samples were resuspended in ethyl acetate and injected into a GC-MS. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY During the course of the run, temperature was ramped from 40° to 300° C in a CH:CHROMATOGRAPHY_SUMMARY 16 minute period. CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Agilent DB5-MS (15m) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Area MS_METABOLITE_DATA_START Samples 15298 15862 16710 17024 17122 17234 17585 17587 17721 17817 17848 17879 17891 17893 17897 17902 17962 17985 18004 18010 18013 18014 18018 18020 18030 18035 18054 18056 18061 18062 18063 18064 18072 18073 18077 18083 18091 18097 18098 18102 18106 18112 18137 18140 18154 18156 18162 18174 18175 18225 18240 18250 18261 18262 18265 18277 18317 18331 18415 18469 18489 18542 18613 18661 18734 18742 18830 18850 18882 18887 18901 18918 18998 19034 19049 19169 Factors Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:African American Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Case control | RACE:- Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:Caucasian Diagnosis:Prostate cancer | RACE:African American Diagnosis:Prostate cancer | RACE:Caucasian sarcosine 0.306212115 0.036214891 0.060943198 0.030796403 0.064277287 0.06270096 0.041105007 0.02944244 0.089869029 0.053729839 0.02049075 0.023132966 0.060517067 0.009655103 0.081346568 0.030886748 0.046049832 0.508449705 0.012203617 0.084157926 0.034806747 0.105824243 0.05996695 0.074310646 0.015586707 0.017291889 0.068265503 0.038671311 0.028820713 0.026537115 0.061244109 0.049490365 0.04764676 0.057862921 0.02305363 0.015765054 0.151826452 0.062898989 0.064242775 0.027775762 0.09842025 0.007504824 0.026210109 0.034022345 0.03193908 0.031141167 0.032666679 0.044775507 0.078166175 0.077460995 0.060020378 0.013411893 0.018684339 0.038028623 0.010864089 0.047361123 0.012271321 0.081980337 0.092541526 0.016046688 0.060564506 0.01506612 0.02423258 0.005474469 0.038386821 0.047843915 0.047869209 0.036376335 0.037731801 0.12699958 0.060098705 0.11419193 0.048223421 0.040516974 0.016713836 0.262978185 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Kegg ID PubChem quantitated m/z Retention time sarcosine C00213 3513 161 4 METABOLITES_END #END