#METABOLOMICS WORKBENCH ppzhang_20190205_184541 DATATRACK_ID:1616 STUDY_ID:ST001132 ANALYSIS_ID:AN001857 PROJECT_ID:PR000757 VERSION 1 CREATED_ON February 6, 2019, 12:29 pm #PROJECT PR:PROJECT_TITLE Investigate the False Discovery in Biomarker Research Using LC-HRMS based PR:PROJECT_TITLE Untargeted Metabolomics Profiling PR:PROJECT_SUMMARY Pooled human plasma was spiked separately with two different sets of 11 PR:PROJECT_SUMMARY metabolite standards (22 “true biomarkers”) to mimic plasma samples PR:PROJECT_SUMMARY collected from diseased subjects and non-diseased subjects. Metabolite extracts PR:PROJECT_SUMMARY of individual samples were subjected to biomarker discovery using LC-HRMS. PR:INSTITUTE University of Macau, Macau, China PR:DEPARTMENT Institute of Translational Medicine, Faculty of Health Sciences, PR:LABORATORY Pilot Laboratory PR:LAST_NAME ZHANG PR:FIRST_NAME pw PR:ADDRESS Taipa PR:EMAIL yb47620@um.edu.mo PR:PHONE 88222534 PR:FUNDING_SOURCE University of Macau #STUDY ST:STUDY_TITLE Investigate the False Discovery in Biomarker Research Using LC-HRMS based ST:STUDY_TITLE Untargeted Metabolomics Profiling ST:STUDY_TYPE mimicking metabolomics study ST:STUDY_SUMMARY Pooled human plasma was spiked separately with two different sets of 11 ST:STUDY_SUMMARY metabolite standards (22 “true biomarkers”) to mimic plasma samples ST:STUDY_SUMMARY collected from diseased subjects and non-diseased subjects. Metabolite extracts ST:STUDY_SUMMARY of individual samples were subjected to biomarker discovery using LC-HRMS. ST:INSTITUTE University of Macau, Macau, China ST:DEPARTMENT Institute of Translational Medicine, Faculty of Health Sciences, ST:LABORATORY Pilot Laboratory ST:LAST_NAME ZHANG ST:FIRST_NAME pw ST:ADDRESS Taipa ST:EMAIL yb47620@um.edu.mo ST:PHONE 88222534 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENDER Pooled #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - A1 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A2 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A3 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A4 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A5 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A6 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A7 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A8 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A9 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A10 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A11 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - A12 SampleType:spiked SetA SUBJECT_SAMPLE_FACTORS - B1 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B2 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B3 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B4 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B5 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B6 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B7 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B8 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B9 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B10 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B11 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - B12 SampleType:spiked SetB SUBJECT_SAMPLE_FACTORS - Negative control1 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control2 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control3 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control4 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control5 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control6 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control7 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control8 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control9 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control10 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control11 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control12 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control13 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control14 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control15 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control16 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control17 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control18 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control19 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control20 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control21 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control22 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control23 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - Negative control24 SampleType:no treatment SUBJECT_SAMPLE_FACTORS - QC1 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC2 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC3 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC4 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC5 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC6 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC7 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC8 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC9 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC10 SampleType:QC SUBJECT_SAMPLE_FACTORS - QC11 SampleType:QC SUBJECT_SAMPLE_FACTORS - Blank1 SampleType:blank SUBJECT_SAMPLE_FACTORS - Blank2 SampleType:blank #COLLECTION CO:COLLECTION_SUMMARY Pooled human potassium EDTA plasma was purchased from a commercial company CO:COLLECTION_SUMMARY (Equitech-Bio Inc., Kerrville, TX, USA) CO:SAMPLE_TYPE Blood (plasma) CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Mimicking diseased plasma samples and non-diseased samples (12 samples for each TR:TREATMENT_SUMMARY group) were spiked with Set A and Set B metabolite standards, respectively. Two TR:TREATMENT_SUMMARY groups of negative control samples (12 samples for each group) were also TR:TREATMENT_SUMMARY prepared, but replacing Set A and Set B metabolite standard mixtures with LC-MS TR:TREATMENT_SUMMARY grade water. Information of the two sets of metabolite standards spiked into the TR:TREATMENT_SUMMARY human pooled plasma. Set A (metabolite standard spiked concentration μM): TR:TREATMENT_SUMMARY L-Leucine 250,Creatine 110, L-Histidine 160, L-Phenylalanine 130, D-(+)-Glucose TR:TREATMENT_SUMMARY 10000, L-Aspartic Acid 40, L-Valine 460, L-Alanine 660, L-Serine 280, TR:TREATMENT_SUMMARY L-Carnitine 90, L-Glutamine 1180. Set B (metabolite standard spiked TR:TREATMENT_SUMMARY concentration μM): Creatinine 150, L-Proline 480, Betaine 150, L-Glycine 460, TR:TREATMENT_SUMMARY L-Arginine 220, L-Threonine 280, L-Tryptophan 100, L-Lysine 360, L-Glutamic Acid TR:TREATMENT_SUMMARY 170, L-Asparagine 80, Hypoxanthine 20. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 1. Preparation of Metabolite Standard Spiked Plasma Samples for the Biomarker SP:SAMPLEPREP_SUMMARY Discovery Experiment Individual metabolite standard solutions were prepared in SP:SAMPLEPREP_SUMMARY LC-MS grade water. Each set of metabolite standards was prepared separately by SP:SAMPLEPREP_SUMMARY mixing equal volumes of 11 metabolite standards. The two metabolite mixtures was SP:SAMPLEPREP_SUMMARY dried by speed vacuum at room temperature, and redissolved separately in the SP:SAMPLEPREP_SUMMARY human pooled plasma to form two master spiked plasma samples. Each of the two SP:SAMPLEPREP_SUMMARY master spiked plasma samples was divided into 12 identical aliquots (each 30 SP:SAMPLEPREP_SUMMARY µL), which were treated as plasma samples collected from 12 different people. SP:SAMPLEPREP_SUMMARY The quality control (QC) sample was prepared by mixing equal amount of solutions SP:SAMPLEPREP_SUMMARY of each spiked plasma sample, and it was used to check the stability of the SP:SAMPLEPREP_SUMMARY system throughout the sequence analysis. 2. Preparation of Plasma Samples for SP:SAMPLEPREP_SUMMARY the Negative Control Experiment Two groups of negative control samples (12 SP:SAMPLEPREP_SUMMARY identical samples for each group) were prepared according to the above strategy, SP:SAMPLEPREP_SUMMARY but replacing Set A and Set B metabolite standard mixtures with LC-MS grade SP:SAMPLEPREP_SUMMARY water. 3. Preparation of Blank Sample The solvent extraction blank samples were SP:SAMPLEPREP_SUMMARY prepared according to the plasma metabolite extraction procedure, but replacing SP:SAMPLEPREP_SUMMARY plasma with equal volume of MS grade water. 4. Plasma Metabolite Extraction SP:SAMPLEPREP_SUMMARY Frozen pooled plasma samples were thawed at 4 oC and vortexed for 30 seconds SP:SAMPLEPREP_SUMMARY before metabolite extraction. Thirty microliters of plasma were mixed with 120 SP:SAMPLEPREP_SUMMARY µL chilled methanol, and vortexed for 30 seconds. The mixture was incubated at SP:SAMPLEPREP_SUMMARY 4 oC for 20 minutes to precipitate the proteins. After incubation, the mixture SP:SAMPLEPREP_SUMMARY was centrifuged at 14,000 g for 10 min to pellet the proteins. The supernatant SP:SAMPLEPREP_SUMMARY were recovered as the metabolite extract, and stored at -80 oC before LC-HRMS SP:SAMPLEPREP_SUMMARY analysis. SP:PROCESSING_STORAGE_CONDITIONS 4℃ SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Individual metabolite extracts were separated on an amide HILIC (Accucore™ 150 CH:CHROMATOGRAPHY_SUMMARY Amide HILIC 2.1×150 mm, Thermo Fisher) column at a flow rate of 0.3 mL/min CH:CHROMATOGRAPHY_SUMMARY using a UHPLC system (Dionex UltiMate 3000, Thermo Fisher).The optimized CH:CHROMATOGRAPHY_SUMMARY stepwise linear gradient:10% B in the first 2 min, 10% - 30% B in the next 5 CH:CHROMATOGRAPHY_SUMMARY min, followed by 30% - 60% in 3 min, and finally 60% - 90% in 5 min. CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 RS CH:COLUMN_NAME Unspecified CH:FLOW_RATE 0.3 ml/min CH:COLUMN_TEMPERATURE 30 CH:METHODS_FILENAME Chromatography CH:SOLVENT_A 98% acetonitrile, 2% water and 0.1% formic acid CH:SOLVENT_B 98% water, 2% acetonitrile, 30 mM ammonium formate and 0.1% formic acid CH:INJECTION_TEMPERATURE 8 CH:SAMPLE_INJECTION 2 micro litter CH:ANALYTICAL_TIME 21 min CH:CAPILLARY_VOLTAGE 320 CH:PRECONDITIONING 1h #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS spray voltage, 3.5 kV; capillary temperature, 320 °C; sheath gas flow rate, 45; MS:MS_COMMENTS auxiliary gas flow rate, 25; heater temperature 350 °C; AGC, 3×106; maximum MS:MS_COMMENTS injection time, 200 ms; mass scan range, 50–750; full MS resolution, 70,000 MS:MS_COMMENTS FWHM at m/z 200; spectrum data type, profile. MS:MS_RESULTS_FILE ST001132_AN001857_Results.txt UNITS:ARBITRARY Has m/z:Yes Has RT:Yes RT units:Minutes #END