{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001641","ANALYSIS_ID":"AN002686","VERSION":"1","CREATED_ON":"January 8, 2021, 2:24 pm"},

"PROJECT":{"PROJECT_TITLE":"Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular Carcinoma.","PROJECT_SUMMARY":"Comparing blood lipidomics of healthy volunteers to patients with chronic liver disease (CLD), and to patients with HCC caused by viral infections. We contrasted our findings in blood to lipid alterations in liver tumor and nontumor tissue samples from HCC patients.","INSTITUTE":"West coast metabolomics center","LAST_NAME":"Ismail","FIRST_NAME":"Israa","ADDRESS":"415 health science drive, 95616 ,Davis, California, USA.","EMAIL":"Israataher2015@gmail.com","PHONE":"01 530 7613155"},

"STUDY":{"STUDY_TITLE":"Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular Carcinoma (Liver) - part II","STUDY_SUMMARY":"Comparing blood lipidomics of healthy volunteers to patients with chronic liver disease (CLD), and to patients with HCC caused by viral infections. We contrasted our findings in blood to lipid alterations in liver tumor and nontumor tissue samples from HCC patients.","INSTITUTE":"University of California, Davis","DEPARTMENT":"West coast metabolomics center","LABORATORY":"Fiehn lab","LAST_NAME":"Ismail","FIRST_NAME":"Israa","ADDRESS":"451 health science drive, 95616 ,Davis, California, USA.","EMAIL":"Israataher2015@gmail.com","PHONE":"01 530 7613155"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"human liver",
"Sample ID":"1 T_054",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver010_MX493661_posCSH_1-T-054.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"2 T_055",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver014_MX493661_posCSH_2-T-055.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"3 T_056",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver036_MX493661_posCSH_3-T-056.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"4 T_057",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver028_MX493661_posCSH_4-T-057.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"5 T_058",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver011_MX493661_posCSH_5-T-058.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"6 T_059",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver008_MX493661_posCSH_6-T-059.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"7 T_060",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver041_MX493661_posCSH_7-T-060.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"8 T_061",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver005_MX493661_posCSH_8-T-061.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"9 T_062",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver016_MX493661_posCSH_9-T-062.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"10 T_063",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver023_MX493661_posCSH_10-T-063.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"11 T_064",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver037_MX493661_posCSH_11-T-064.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"12 T_065",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver021_MX493661_posCSH_12-T-065.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"13 T_066",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver044_MX493661_posCSH_13-T-066.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"14 T_067",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver017_MX493661_posCSH_14-T-067.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"15 T_068",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver025_MX493661_posCSH_15-T-068.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"16 T_069",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver001_MX493661_posCSH_16-T-069.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"17 T_070",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver027_MX493661_posCSH_17-T-070.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"18 T_071",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver029_MX493661_posCSH_18-T-071.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"19 T_072",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver004_MX493661_posCSH_19-T-072.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"20 T_073",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver024_MX493661_posCSH_20-T-073.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"21 T_074",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver035_MX493661_posCSH_21-T-074.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"22 T_075",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver020_MX493661_posCSH_22-T-075.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"23 T_076",
"Factors":{"Sample Source":"tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver045_MX493661_posCSH_23-T-076.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"1 NT_077",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver033_MX493661_posCSH_1-NT-077.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"2 NT_078",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver031_MX493661_posCSH_2-NT-078.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"3 NT_079",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver026_MX493661_posCSH_3-NT-079.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"4 NT_080",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver012_MX493661_posCSH_4-NT-080.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"5 NT_081",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver019_MX493661_posCSH_5-NT-081.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"6 NT_082",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver043_MX493661_posCSH_6-NT-082.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"7 NT_083",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver046_MX493661_posCSH_7-NT-083.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"8 NT_084",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver038_MX493661_posCSH_8-NT-084.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"9 NT_085",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver013_MX493661_posCSH_9-NT-085.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"10 NT_086",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver002_MX493661_posCSH_10-NT-086.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"11 NT_087",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver039_MX493661_posCSH_11-NT-087.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"12 NT_088",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver034_MX493661_posCSH_12-NT-088.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"13 NT_089",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver040_MX493661_posCSH_13-NT-089.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"14 NT_090",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver018_MX493661_posCSH_14-NT-090.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"15 NT_091",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver009_MX493661_posCSH_15-NT-091.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"16 NT_092",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver006_MX493661_posCSH_16-NT-092.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"17 NT_093",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver042_MX493661_posCSH_17-NT-093.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"18 NT_094",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver030_MX493661_posCSH_18-NT-094.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"19 NT_095",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver003_MX493661_posCSH_19-NT-095.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"20 NT_096",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver032_MX493661_posCSH_20-NT-096.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"21 NT_097",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver015_MX493661_posCSH_21-NT-097.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"22 NT_098",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver022_MX493661_posCSH_22-NT-098.d"}
},
{
"Subject ID":"human liver",
"Sample ID":"23 NT_099",
"Factors":{"Sample Source":"non tumor"},
"Additional sample data":{"RAW_FILE_NAME":"TaherLiver007_MX493661_posCSH_23-NT-099.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"human liver samples were collected to compare tumor versus nontumor","SAMPLE_TYPE":"Liver"},

"TREATMENT":{"TREATMENT_SUMMARY":"comparison of tumor versus nontumor patients"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The LC/QTOFMS analyses are performed using an Agilent 1290 Infinity LC system (G4220A binary pump, G4226A autosampler, and G1316C Column Thermostat) coupled to either an Agilent 6530 (positive ion mode) or an Agilent 6550 mass spectrometer equipped with an ion funnel (iFunnel) (negative ion mode). Lipids are separated on an Acquity UPLC CSH C18 column (100 x 2.1 mm; 1.7 µm) maintained at 65°C at a flow-rate of 0.6 mL/min. Solvent pre-heating (Agilent G1316) was used. The mobile phases consist of 60:40 acetonitrile:water with 10 mM ammonium formate and 0.1% formic acid (A) and 90:10 propan-2-ol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid. The gradient is as follows: 0 min 85% (A); 0–2 min 70% (A); 2–2.5 min 52% (A); 2.5–11 min 18% (A); 11–11.5 min 1% (A); 11.5–12 min 1% (A); 12–12.1 min 85% (A); 12.1–15 min 85% (A). A sample volume of 3 µL is used for the injection. Sample temperature is maintained at 4°C in the autosampler.","CHROMATOGRAPHY_TYPE":"Normal phase","INSTRUMENT_NAME":"Agilent","COLUMN_NAME":"Acquity UPLC CSH C18 column"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6550 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"For the data processing the MassHunter software is used, and a unique ID is given to each lipid based on its retention time and exact mass (RT_mz). This allows the report of peak areas/heights or concentration of lipids based on the use of particular internal standards. Lipids are identified based on their unique MS/MS fragmentation patterns using in-house software, Lipidblast. Using complex lipid class-specific internal standards this approach is used to quantify >400 lipid species including: mono-, di- and triacylglycerols, glycerophospholipids, sphingolipids, cholesterol esters, ceramides, and fatty acids.","MS_RESULTS_FILE":"ST001641_AN002686_Results.txt UNITS:counts per second Has m/z:Yes Has RT:Yes RT units:Minutes"}

}