#METABOLOMICS WORKBENCH kpaglia_20210106_130010 DATATRACK_ID:2382 STUDY_ID:ST001641 ANALYSIS_ID:AN002686 PROJECT_ID:000000 VERSION 1 CREATED_ON January 8, 2021, 2:24 pm #PROJECT PR:PROJECT_TITLE Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular PR:PROJECT_TITLE Carcinoma. PR:PROJECT_SUMMARY Comparing blood lipidomics of healthy volunteers to patients with chronic liver PR:PROJECT_SUMMARY disease (CLD), and to patients with HCC caused by viral infections. We PR:PROJECT_SUMMARY contrasted our findings in blood to lipid alterations in liver tumor and PR:PROJECT_SUMMARY nontumor tissue samples from HCC patients. PR:INSTITUTE West coast metabolomics center PR:LAST_NAME Ismail PR:FIRST_NAME Israa PR:ADDRESS 415 health science drive, 95616 ,Davis, California, USA. PR:EMAIL Israataher2015@gmail.com PR:PHONE 01 530 7613155 #STUDY ST:STUDY_TITLE Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular ST:STUDY_TITLE Carcinoma (Liver) - part II ST:STUDY_SUMMARY Comparing blood lipidomics of healthy volunteers to patients with chronic liver ST:STUDY_SUMMARY disease (CLD), and to patients with HCC caused by viral infections. We ST:STUDY_SUMMARY contrasted our findings in blood to lipid alterations in liver tumor and ST:STUDY_SUMMARY nontumor tissue samples from HCC patients. ST:INSTITUTE University of California, Davis ST:DEPARTMENT West coast metabolomics center ST:LABORATORY Fiehn lab ST:LAST_NAME Ismail ST:FIRST_NAME Israa ST:ADDRESS 451 health science drive, 95616 ,Davis, California, USA. ST:EMAIL Israataher2015@gmail.com ST:PHONE 01 530 7613155 #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]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS human liver 1 T_054 Sample Source:tumor RAW_FILE_NAME=TaherLiver010_MX493661_posCSH_1-T-054.d SUBJECT_SAMPLE_FACTORS human liver 2 T_055 Sample Source:tumor RAW_FILE_NAME=TaherLiver014_MX493661_posCSH_2-T-055.d SUBJECT_SAMPLE_FACTORS human liver 3 T_056 Sample Source:tumor RAW_FILE_NAME=TaherLiver036_MX493661_posCSH_3-T-056.d SUBJECT_SAMPLE_FACTORS human liver 4 T_057 Sample Source:tumor RAW_FILE_NAME=TaherLiver028_MX493661_posCSH_4-T-057.d SUBJECT_SAMPLE_FACTORS human liver 5 T_058 Sample Source:tumor RAW_FILE_NAME=TaherLiver011_MX493661_posCSH_5-T-058.d SUBJECT_SAMPLE_FACTORS human liver 6 T_059 Sample Source:tumor RAW_FILE_NAME=TaherLiver008_MX493661_posCSH_6-T-059.d SUBJECT_SAMPLE_FACTORS human liver 7 T_060 Sample Source:tumor RAW_FILE_NAME=TaherLiver041_MX493661_posCSH_7-T-060.d SUBJECT_SAMPLE_FACTORS human liver 8 T_061 Sample Source:tumor RAW_FILE_NAME=TaherLiver005_MX493661_posCSH_8-T-061.d SUBJECT_SAMPLE_FACTORS human liver 9 T_062 Sample Source:tumor RAW_FILE_NAME=TaherLiver016_MX493661_posCSH_9-T-062.d SUBJECT_SAMPLE_FACTORS human liver 10 T_063 Sample Source:tumor RAW_FILE_NAME=TaherLiver023_MX493661_posCSH_10-T-063.d SUBJECT_SAMPLE_FACTORS human liver 11 T_064 Sample Source:tumor RAW_FILE_NAME=TaherLiver037_MX493661_posCSH_11-T-064.d SUBJECT_SAMPLE_FACTORS human liver 12 T_065 Sample Source:tumor RAW_FILE_NAME=TaherLiver021_MX493661_posCSH_12-T-065.d SUBJECT_SAMPLE_FACTORS human liver 13 T_066 Sample Source:tumor RAW_FILE_NAME=TaherLiver044_MX493661_posCSH_13-T-066.d SUBJECT_SAMPLE_FACTORS human liver 14 T_067 Sample Source:tumor RAW_FILE_NAME=TaherLiver017_MX493661_posCSH_14-T-067.d SUBJECT_SAMPLE_FACTORS human liver 15 T_068 Sample Source:tumor RAW_FILE_NAME=TaherLiver025_MX493661_posCSH_15-T-068.d SUBJECT_SAMPLE_FACTORS human liver 16 T_069 Sample Source:tumor RAW_FILE_NAME=TaherLiver001_MX493661_posCSH_16-T-069.d SUBJECT_SAMPLE_FACTORS human liver 17 T_070 Sample Source:tumor RAW_FILE_NAME=TaherLiver027_MX493661_posCSH_17-T-070.d SUBJECT_SAMPLE_FACTORS human liver 18 T_071 Sample Source:tumor RAW_FILE_NAME=TaherLiver029_MX493661_posCSH_18-T-071.d SUBJECT_SAMPLE_FACTORS human liver 19 T_072 Sample Source:tumor RAW_FILE_NAME=TaherLiver004_MX493661_posCSH_19-T-072.d SUBJECT_SAMPLE_FACTORS human liver 20 T_073 Sample Source:tumor RAW_FILE_NAME=TaherLiver024_MX493661_posCSH_20-T-073.d SUBJECT_SAMPLE_FACTORS human liver 21 T_074 Sample Source:tumor RAW_FILE_NAME=TaherLiver035_MX493661_posCSH_21-T-074.d SUBJECT_SAMPLE_FACTORS human liver 22 T_075 Sample Source:tumor RAW_FILE_NAME=TaherLiver020_MX493661_posCSH_22-T-075.d SUBJECT_SAMPLE_FACTORS human liver 23 T_076 Sample Source:tumor RAW_FILE_NAME=TaherLiver045_MX493661_posCSH_23-T-076.d SUBJECT_SAMPLE_FACTORS human liver 1 NT_077 Sample Source:non tumor RAW_FILE_NAME=TaherLiver033_MX493661_posCSH_1-NT-077.d SUBJECT_SAMPLE_FACTORS human liver 2 NT_078 Sample Source:non tumor RAW_FILE_NAME=TaherLiver031_MX493661_posCSH_2-NT-078.d SUBJECT_SAMPLE_FACTORS human liver 3 NT_079 Sample Source:non tumor RAW_FILE_NAME=TaherLiver026_MX493661_posCSH_3-NT-079.d SUBJECT_SAMPLE_FACTORS human liver 4 NT_080 Sample Source:non tumor RAW_FILE_NAME=TaherLiver012_MX493661_posCSH_4-NT-080.d SUBJECT_SAMPLE_FACTORS human liver 5 NT_081 Sample Source:non tumor RAW_FILE_NAME=TaherLiver019_MX493661_posCSH_5-NT-081.d SUBJECT_SAMPLE_FACTORS human liver 6 NT_082 Sample Source:non tumor RAW_FILE_NAME=TaherLiver043_MX493661_posCSH_6-NT-082.d SUBJECT_SAMPLE_FACTORS human liver 7 NT_083 Sample Source:non tumor RAW_FILE_NAME=TaherLiver046_MX493661_posCSH_7-NT-083.d SUBJECT_SAMPLE_FACTORS human liver 8 NT_084 Sample Source:non tumor RAW_FILE_NAME=TaherLiver038_MX493661_posCSH_8-NT-084.d SUBJECT_SAMPLE_FACTORS human liver 9 NT_085 Sample Source:non tumor RAW_FILE_NAME=TaherLiver013_MX493661_posCSH_9-NT-085.d SUBJECT_SAMPLE_FACTORS human liver 10 NT_086 Sample Source:non tumor RAW_FILE_NAME=TaherLiver002_MX493661_posCSH_10-NT-086.d SUBJECT_SAMPLE_FACTORS human liver 11 NT_087 Sample Source:non tumor RAW_FILE_NAME=TaherLiver039_MX493661_posCSH_11-NT-087.d SUBJECT_SAMPLE_FACTORS human liver 12 NT_088 Sample Source:non tumor RAW_FILE_NAME=TaherLiver034_MX493661_posCSH_12-NT-088.d SUBJECT_SAMPLE_FACTORS human liver 13 NT_089 Sample Source:non tumor RAW_FILE_NAME=TaherLiver040_MX493661_posCSH_13-NT-089.d SUBJECT_SAMPLE_FACTORS human liver 14 NT_090 Sample Source:non tumor RAW_FILE_NAME=TaherLiver018_MX493661_posCSH_14-NT-090.d SUBJECT_SAMPLE_FACTORS human liver 15 NT_091 Sample Source:non tumor RAW_FILE_NAME=TaherLiver009_MX493661_posCSH_15-NT-091.d SUBJECT_SAMPLE_FACTORS human liver 16 NT_092 Sample Source:non tumor RAW_FILE_NAME=TaherLiver006_MX493661_posCSH_16-NT-092.d SUBJECT_SAMPLE_FACTORS human liver 17 NT_093 Sample Source:non tumor RAW_FILE_NAME=TaherLiver042_MX493661_posCSH_17-NT-093.d SUBJECT_SAMPLE_FACTORS human liver 18 NT_094 Sample Source:non tumor RAW_FILE_NAME=TaherLiver030_MX493661_posCSH_18-NT-094.d SUBJECT_SAMPLE_FACTORS human liver 19 NT_095 Sample Source:non tumor RAW_FILE_NAME=TaherLiver003_MX493661_posCSH_19-NT-095.d SUBJECT_SAMPLE_FACTORS human liver 20 NT_096 Sample Source:non tumor RAW_FILE_NAME=TaherLiver032_MX493661_posCSH_20-NT-096.d SUBJECT_SAMPLE_FACTORS human liver 21 NT_097 Sample Source:non tumor RAW_FILE_NAME=TaherLiver015_MX493661_posCSH_21-NT-097.d SUBJECT_SAMPLE_FACTORS human liver 22 NT_098 Sample Source:non tumor RAW_FILE_NAME=TaherLiver022_MX493661_posCSH_22-NT-098.d SUBJECT_SAMPLE_FACTORS human liver 23 NT_099 Sample Source:non tumor RAW_FILE_NAME=TaherLiver007_MX493661_posCSH_23-NT-099.d #COLLECTION CO:COLLECTION_SUMMARY human liver samples were collected to compare tumor versus nontumor CO:SAMPLE_TYPE Liver #TREATMENT TR:TREATMENT_SUMMARY comparison of tumor versus nontumor patients #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL SP:SAMPLEPREP_SUMMARY extraction solvent to the tissue sample and homogenize for 45 seconds ensuring SP:SAMPLEPREP_SUMMARY that sample resembles a powder. In between samples, clean the homogenizer in SP:SAMPLEPREP_SUMMARY solutions of methanol, acetone, water, and the extraction solvent in the order SP:SAMPLEPREP_SUMMARY listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge SP:SAMPLEPREP_SUMMARY the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for SP:SAMPLEPREP_SUMMARY analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. SP:SAMPLEPREP_SUMMARY Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap SP:SAMPLEPREP_SUMMARY concentrator to complete dryness (typically overnight). The dried aliquot is SP:SAMPLEPREP_SUMMARY then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge SP:SAMPLEPREP_SUMMARY for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove SP:SAMPLEPREP_SUMMARY supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the SP:SAMPLEPREP_SUMMARY the Labconco Centrivap cold trap concentrator. Submit to derivatization. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY The LC/QTOFMS analyses are performed using an Agilent 1290 Infinity LC system CH:CHROMATOGRAPHY_SUMMARY (G4220A binary pump, G4226A autosampler, and G1316C Column Thermostat) coupled CH:CHROMATOGRAPHY_SUMMARY to either an Agilent 6530 (positive ion mode) or an Agilent 6550 mass CH:CHROMATOGRAPHY_SUMMARY spectrometer equipped with an ion funnel (iFunnel) (negative ion mode). Lipids CH:CHROMATOGRAPHY_SUMMARY are separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) CH:CHROMATOGRAPHY_SUMMARY maintained at 65°C at a flow-rate of 0.6 mL/min. Solvent pre-heating (Agilent CH:CHROMATOGRAPHY_SUMMARY G1316) was used. The mobile phases consist of 60:40 acetonitrile:water with 10 CH:CHROMATOGRAPHY_SUMMARY mM ammonium formate and 0.1% formic acid (A) and 90:10 propan-2-ol:acetonitrile CH:CHROMATOGRAPHY_SUMMARY with 10 mM ammonium formate and 0.1% formic acid. The gradient is as follows: 0 CH:CHROMATOGRAPHY_SUMMARY min 85% (A); 0–2 min 70% (A); 2–2.5 min 52% (A); 2.5–11 min 18% (A); CH:CHROMATOGRAPHY_SUMMARY 11–11.5 min 1% (A); 11.5–12 min 1% (A); 12–12.1 min 85% (A); 12.1–15 min CH:CHROMATOGRAPHY_SUMMARY 85% (A). A sample volume of 3 µL is used for the injection. Sample temperature CH:CHROMATOGRAPHY_SUMMARY is maintained at 4°C in the autosampler. CH:CHROMATOGRAPHY_TYPE Normal phase CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Acquity UPLC CSH C18 column #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6550 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE EI MS:ION_MODE POSITIVE MS:MS_COMMENTS For the data processing the MassHunter software is used, and a unique ID is MS:MS_COMMENTS given to each lipid based on its retention time and exact mass (RT_mz). This MS:MS_COMMENTS allows the report of peak areas/heights or concentration of lipids based on the MS:MS_COMMENTS use of particular internal standards. Lipids are identified based on their MS:MS_COMMENTS unique MS/MS fragmentation patterns using in-house software, Lipidblast. Using MS:MS_COMMENTS complex lipid class-specific internal standards this approach is used to MS:MS_COMMENTS quantify >400 lipid species including: mono-, di- and triacylglycerols, MS:MS_COMMENTS glycerophospholipids, sphingolipids, cholesterol esters, ceramides, and fatty MS:MS_COMMENTS acids. MS:MS_RESULTS_FILE ST001641_AN002686_Results.txt UNITS:counts per second Has m/z:Yes Has RT:Yes RT units:Minutes #END