#METABOLOMICS WORKBENCH fernandezlab_20181019_121839 DATATRACK_ID:1550 STUDY_ID:ST001081 ANALYSIS_ID:AN001765 PROJECT_ID:PR000724 VERSION 1 CREATED_ON October 29, 2018, 12:05 pm #PROJECT PR:PROJECT_TITLE Preoperative Metabolic Signatures of Prostate Cancer Recurrence Following PR:PROJECT_TITLE Radical Prostatectomy PR:PROJECT_SUMMARY Prostate cancer patient serum was analyzed using HILIC and RP LC/MS and NMR. PR:INSTITUTE Georgia Institute of Technology PR:LAST_NAME Fernandez PR:FIRST_NAME Facundo PR:ADDRESS 901 Atlantic Dr NE, Atlanta, GA, 30332, USA PR:EMAIL fernandez@gatech.edu PR:PHONE 404-385-4432 #STUDY ST:STUDY_TITLE Combined NMR and MS Analysis of PC patient serum ST:STUDY_SUMMARY Serum of two groups of patients were analyzed using MS and NMR to find ST:STUDY_SUMMARY predictive markers of recurrence ST:INSTITUTE Georgia Institute of Technology ST:DEPARTMENT Department of Chemistry ST:LABORATORY Fernandez ST:LAST_NAME Fernandez ST:FIRST_NAME Facundo ST:ADDRESS 901 Atlantic Dr NE, Atlanta, GA, 30332, USA ST:EMAIL fernandez@gatech.edu ST:PHONE 404-385-4432 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 80 ST:NUM_MALES 80 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:AGE_OR_AGE_RANGE 44-70 SU:GENDER Male SU:HUMAN_INCLUSION_CRITERIA Prostatectomy patients #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - b1_2 Sample Type:Blank SUBJECT_SAMPLE_FACTORS - b3 Sample Type:Blank SUBJECT_SAMPLE_FACTORS - sb_f Sample Type:Blank SUBJECT_SAMPLE_FACTORS - sb1 Sample Type:Blank SUBJECT_SAMPLE_FACTORS - P1 Sample Type:Pooled SUBJECT_SAMPLE_FACTORS - P1_2 Sample Type:Pooled SUBJECT_SAMPLE_FACTORS - P2 Sample Type:Pooled SUBJECT_SAMPLE_FACTORS - P2_2 Sample Type:Pooled SUBJECT_SAMPLE_FACTORS - S10_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S10_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S15_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S15_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S25_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S25_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S34_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S34_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S35_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S35_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S37_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S37_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S39_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S39_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S45_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S45_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S48_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S48_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S49_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S49_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S50_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S50_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S51_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S51_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S52_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S52_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S53_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S53_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S54_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S54_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S57_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S57_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S58_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S58_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S59_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S59_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S60_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S60_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S61_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S61_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S62_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S62_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S63_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S63_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S64_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S64_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S65_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S65_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S68_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S68_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S69_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S69_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S71_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S71_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S73_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S73_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S74_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S74_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S75_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S75_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S76_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S76_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S78_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S78_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S79_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S79_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S80_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S80_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S81_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S81_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S82_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S82_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S83_1 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S83_2 Sample Type:Recurrence SUBJECT_SAMPLE_FACTORS - S1_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S1_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S2_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S2_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S3_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S3_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S4_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S4_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S5_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S5_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S6_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S6_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S7_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S7_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S8_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S8_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S9_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S9_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S11_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S11_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S12_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S12_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S13_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S13_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S14_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S14_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S16_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S16_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S17_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S17_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S18_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S18_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S19_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S19_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S20_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S20_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S21_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S21_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S22_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S22_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S23_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S23_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S24_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S24_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S26_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S26_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S27_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S27_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S28_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S28_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S29_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S29_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S30_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S30_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S31_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S31_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S32_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S32_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S33_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S33_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S36_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S36_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S38_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S38_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S41_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S41_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S42_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S42_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S43_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S43_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S44_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S44_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S46_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S46_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S47_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S47_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S66_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S66_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S67_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S67_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S70_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S70_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S72_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S72_2 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S77_1 Sample Type:No Recurrence SUBJECT_SAMPLE_FACTORS - S77_2 Sample Type:No Recurrence #COLLECTION CO:COLLECTION_SUMMARY After Emory Institutional Review Board (IRB) approval, patients were consented CO:COLLECTION_SUMMARY and blood collected in SST Serum Separation Tubes: Hemogard (Fisher Scientific). CO:COLLECTION_SUMMARY Serum was separated by centrifugation at 1300 rcf for 20 min at 4 °C. Serum CO:COLLECTION_SUMMARY aliquots were stored long term in liquid nitrogen until removed for analysis. CO:SAMPLE_TYPE Blood (serum) CO:COLLECTION_LOCATION Emory University CO:COLLECTION_FREQUENCY Pre-operative CO:STORAGE_CONDITIONS Described in summary #TREATMENT TR:TREATMENT_SUMMARY These patients underwent prostatectomy after serum was collected. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Proteins were precipitated from serum samples using either MeOH (for HILIC LC/MS SP:SAMPLEPREP_SUMMARY and NMR) or Isopropanol (for RP LC/MS). Samples stored in -80 until analyzed SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap CH:COLUMN_NAME Waters Acquity BEH C18 (50 x 2.1mm, 1.7um) CH:FLOW_GRADIENT 0-1 min 55% A: 1-1.1 min. 50% A; 1.1-5.0 min 45% A; 5.0-5.1 min 30% A; 5.1-8.0 CH:FLOW_GRADIENT min 1%A; 8.0-8.1 min 60% A; and 8.1-9.5 min held at 60% A CH:FLOW_RATE 400 µL min-1 CH:COLUMN_TEMPERATURE 40 CH:SOLVENT_A 60% ACN: 40% 10 mM NH4HCO2 in H2O with 0.1% H2CO2 CH:SOLVENT_B 0% ACN: 90% IPA 10 mM NH4HCO2 with 0.1% H2CO2 CH:ANALYTICAL_TIME 9.5 min #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_RESULTS_FILE ST001081_AN001765_Results.txt UNITS:Relative abundance #END