#METABOLOMICS WORKBENCH kpaglia_20210104_120810 DATATRACK_ID:2379 STUDY_ID:ST001640 ANALYSIS_ID:AN002685 VERSION 1 CREATED_ON 03-03-2022 #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 University of California, Davis PR:DEPARTMENT West Coast Metabolomics Center PR:LAST_NAME Ismail PR:FIRST_NAME Israa PR:ADDRESS 451 Health Sciences Drive, Room 1313, Davis, CA, 95616, USA PR:EMAIL Israataher2015@gmail.com PR:PHONE 01 530 7613155 PR:FUNDING_SOURCE This research was funded by the U.S. National Institutes of Health, U2C ES030158 PR:FUNDING_SOURCE (to O.F.) and the Egyptian Ministry of Higher Education (to I.T.I). PR:DOI http://dx.doi.org/10.21228/M83Q4K #STUDY ST:STUDY_TITLE Remodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular ST:STUDY_TITLE Carcinoma (Blood) - part I 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:LAST_NAME Ismail ST:FIRST_NAME Israa ST:ADDRESS 451 Health Sciences Drive, Room 1313, Davis, CA, 95616, USA ST:EMAIL Israataher2015@gmail.com ST:PHONE 01 530 7613155 ST:SUBMIT_DATE 2021-01-04 #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]Additional sample data SUBJECT_SAMPLE_FACTORS - 16P_016 Treatment:CLD RAW_FILE_NAME=TaherPlasma019_MX493661_posCSH_16-P-016.d SUBJECT_SAMPLE_FACTORS - 17P_017 Treatment:CLD RAW_FILE_NAME=TaherPlasma031_MX493661_posCSH_17-P-017.d SUBJECT_SAMPLE_FACTORS - 18P_018 Treatment:CLD RAW_FILE_NAME=TaherPlasma036_MX493661_posCSH_18-P-018.d SUBJECT_SAMPLE_FACTORS - 19P_019 Treatment:CLD RAW_FILE_NAME=TaherPlasma020_MX493661_posCSH_19-P-019.d SUBJECT_SAMPLE_FACTORS - 20P_020 Treatment:CLD RAW_FILE_NAME=TaherPlasma021_MX493661_posCSH_20-P-020.d SUBJECT_SAMPLE_FACTORS - 21P_021 Treatment:CLD RAW_FILE_NAME=TaherPlasma026_MX493661_posCSH_21-P-021.d SUBJECT_SAMPLE_FACTORS - 22P_022 Treatment:CLD RAW_FILE_NAME=TaherPlasma042_MX493661_posCSH_22-P-022.d SUBJECT_SAMPLE_FACTORS - 23P_023 Treatment:CLD RAW_FILE_NAME=TaherPlasma012_MX493661_posCSH_23-P-023.d SUBJECT_SAMPLE_FACTORS - 24P_024 Treatment:CLD RAW_FILE_NAME=TaherPlasma002_MX493661_posCSH_24-P-024.d SUBJECT_SAMPLE_FACTORS - 25P_025 Treatment:CLD RAW_FILE_NAME=TaherPlasma014_MX493661_posCSH_25-P-025.d SUBJECT_SAMPLE_FACTORS - 26P_026 Treatment:CLD RAW_FILE_NAME=TaherPlasma028_MX493661_posCSH_26-P-026.d SUBJECT_SAMPLE_FACTORS - 27P_027 Treatment:CLD RAW_FILE_NAME=TaherPlasma052_MX493661_posCSH_27-P-027.d SUBJECT_SAMPLE_FACTORS - 28P_028 Treatment:CLD RAW_FILE_NAME=TaherPlasma033_MX493661_posCSH_28-P-028.d SUBJECT_SAMPLE_FACTORS - 29P_029 Treatment:CLD RAW_FILE_NAME=TaherPlasma006_MX493661_posCSH_29-P-029.d SUBJECT_SAMPLE_FACTORS - 30P_030 Treatment:CLD RAW_FILE_NAME=TaherPlasma008_MX493661_posCSH_30-P-030.d SUBJECT_SAMPLE_FACTORS - 10P_010 Treatment:Control RAW_FILE_NAME=TaherPlasma038_MX493661_posCSH_10-P-010.d SUBJECT_SAMPLE_FACTORS - 11P_011 Treatment:Control RAW_FILE_NAME=TaherPlasma044_MX493661_posCSH_11-P-011.d SUBJECT_SAMPLE_FACTORS - 12P_012 Treatment:Control RAW_FILE_NAME=TaherPlasma001_MX493661_posCSH_12-P-012.d SUBJECT_SAMPLE_FACTORS - 13P_013 Treatment:Control RAW_FILE_NAME=TaherPlasma016_MX493661_posCSH_13-P-013.d SUBJECT_SAMPLE_FACTORS - 14P_014 Treatment:Control RAW_FILE_NAME=TaherPlasma043_MX493661_posCSH_14-P-014.d SUBJECT_SAMPLE_FACTORS - 15P_015 Treatment:Control RAW_FILE_NAME=TaherPlasma051_MX493661_posCSH_15-P-015.d SUBJECT_SAMPLE_FACTORS - 1P_001 Treatment:Control RAW_FILE_NAME=TaherPlasma017_MX493661_posCSH_1-P-001.d SUBJECT_SAMPLE_FACTORS - 2P_002 Treatment:Control RAW_FILE_NAME=TaherPlasma040_MX493661_posCSH_2-P-002.d SUBJECT_SAMPLE_FACTORS - 3P_003 Treatment:Control RAW_FILE_NAME=TaherPlasma022_MX493661_posCSH_3-P-003.d SUBJECT_SAMPLE_FACTORS - 4P_004 Treatment:Control RAW_FILE_NAME=TaherPlasma007_MX493661_posCSH_4-P-004.d SUBJECT_SAMPLE_FACTORS - 5P_005 Treatment:Control RAW_FILE_NAME=TaherPlasma034_MX493661_posCSH_5-P-005.d SUBJECT_SAMPLE_FACTORS - 6P_006 Treatment:Control RAW_FILE_NAME=TaherPlasma015_MX493661_posCSH_6-P-006.d SUBJECT_SAMPLE_FACTORS - 7P_007 Treatment:Control RAW_FILE_NAME=TaherPlasma048_MX493661_posCSH_7-P-007.d SUBJECT_SAMPLE_FACTORS - 8P_008 Treatment:Control RAW_FILE_NAME=TaherPlasma041_MX493661_posCSH_8-P-008.d SUBJECT_SAMPLE_FACTORS - 9P_009 Treatment:Control RAW_FILE_NAME=TaherPlasma005_MX493661_posCSH_9-P-009.d SUBJECT_SAMPLE_FACTORS - 31P_031 Treatment:HCC RAW_FILE_NAME=TaherPlasma023_MX493661_posCSH_31-P-031.d SUBJECT_SAMPLE_FACTORS - 32P_032 Treatment:HCC RAW_FILE_NAME=TaherPlasma035_MX493661_posCSH_32-P-032.d SUBJECT_SAMPLE_FACTORS - 33P_033 Treatment:HCC RAW_FILE_NAME=TaherPlasma050_MX493661_posCSH_33-P-033.d SUBJECT_SAMPLE_FACTORS - 34P_034 Treatment:HCC RAW_FILE_NAME=TaherPlasma009_MX493661_posCSH_34-P-034.d SUBJECT_SAMPLE_FACTORS - 35P_035 Treatment:HCC RAW_FILE_NAME=TaherPlasma053_MX493661_posCSH_35-P-035.d SUBJECT_SAMPLE_FACTORS - 36P_036 Treatment:HCC RAW_FILE_NAME=TaherPlasma045_MX493661_posCSH_36-P-036.d SUBJECT_SAMPLE_FACTORS - 37P_037 Treatment:HCC RAW_FILE_NAME=TaherPlasma024_MX493661_posCSH_37-P-037.d SUBJECT_SAMPLE_FACTORS - 38P_038 Treatment:HCC RAW_FILE_NAME=TaherPlasma030_MX493661_posCSH_38-P-038.d SUBJECT_SAMPLE_FACTORS - 39P_039 Treatment:HCC RAW_FILE_NAME=TaherPlasma046_MX493661_posCSH_39-P-039.d SUBJECT_SAMPLE_FACTORS - 40P_040 Treatment:HCC RAW_FILE_NAME=TaherPlasma025_MX493661_posCSH_40-P-040.d SUBJECT_SAMPLE_FACTORS - 41P_041 Treatment:HCC RAW_FILE_NAME=TaherPlasma003_MX493661_posCSH_41-P-041.d SUBJECT_SAMPLE_FACTORS - 42P_042 Treatment:HCC RAW_FILE_NAME=TaherPlasma047_MX493661_posCSH_42-P-042.d SUBJECT_SAMPLE_FACTORS - 43P_043 Treatment:HCC RAW_FILE_NAME=TaherPlasma018_MX493661_posCSH_43-P-043.d SUBJECT_SAMPLE_FACTORS - 44P_044 Treatment:HCC RAW_FILE_NAME=TaherPlasma010_MX493661_posCSH_44-P-044.d SUBJECT_SAMPLE_FACTORS - 45P_045 Treatment:HCC RAW_FILE_NAME=TaherPlasma011_MX493661_posCSH_45-P-045.d SUBJECT_SAMPLE_FACTORS - 46P_046 Treatment:HCC RAW_FILE_NAME=TaherPlasma049_MX493661_posCSH_46-P-046.d SUBJECT_SAMPLE_FACTORS - 47P_047 Treatment:HCC RAW_FILE_NAME=TaherPlasma037_MX493661_posCSH_47-P-047.d SUBJECT_SAMPLE_FACTORS - 48P_048 Treatment:HCC RAW_FILE_NAME=TaherPlasma027_MX493661_posCSH_48-P-048.d SUBJECT_SAMPLE_FACTORS - 49P_049 Treatment:HCC RAW_FILE_NAME=TaherPlasma032_MX493661_posCSH_49-P-049.d SUBJECT_SAMPLE_FACTORS - 50P_050 Treatment:HCC RAW_FILE_NAME=TaherPlasma039_MX493661_posCSH_50-P-050.d SUBJECT_SAMPLE_FACTORS - 51P_051 Treatment:HCC RAW_FILE_NAME=TaherPlasma004_MX493661_posCSH_51-P-051.d SUBJECT_SAMPLE_FACTORS - 52P_052 Treatment:HCC RAW_FILE_NAME=TaherPlasma029_MX493661_posCSH_52-P-052.d SUBJECT_SAMPLE_FACTORS - 53P_053 Treatment:HCC RAW_FILE_NAME=TaherPlasma013_MX493661_posCSH_53-P-053.d #COLLECTION CO:COLLECTION_SUMMARY Samples of both plasma and liver were collected from healthy patients and CO:COLLECTION_SUMMARY patients with chronic liver diseases. CO:SAMPLE_TYPE Blood (plasma) #TREATMENT TR:TREATMENT_SUMMARY Healthy patients (control) versus CLD and HCC for plasma. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Extraction of plasma lipids is based on the “Maytash'' method [1] which was SP:SAMPLEPREP_SUMMARY subsequently modified. Extraction is carried out using a bi-phasic solvent SP:SAMPLEPREP_SUMMARY system of cold methanol, methyl tert-butyl ether (MTBE), and water. In more SP:SAMPLEPREP_SUMMARY detail, cold methanol (225 µL) containing a mixture of odd chain and deuterated SP:SAMPLEPREP_SUMMARY lipid internal standards [lysoPE(17:1), lysoPC(17:0), PC(12:0/13:0), SP:SAMPLEPREP_SUMMARY PE(17:0/17:0), PG(17:0/17:0), sphingosine (d17:1), d7-cholesterol, SM(17:0), C17 SP:SAMPLEPREP_SUMMARY ceramide, d3-palmitic acid, MG(17:0/0:0/0:0), DG(18:1/2:0/0:0), SP:SAMPLEPREP_SUMMARY DG(12:0/12:0/0:0), and d5-TG(17:0/17:1/17:0)] is added to a 20 µL sample SP:SAMPLEPREP_SUMMARY aliquot, which is placed into a 1.5 mL Eppendorf tube, and the tube is vortexed SP:SAMPLEPREP_SUMMARY for 10 s. Then, 750 µL of cold MTBE containing CE(22:1) (internal standard) are SP:SAMPLEPREP_SUMMARY added, followed by vortexing for 10 s. and shaking for 6 min. at 4ºC. Phase SP:SAMPLEPREP_SUMMARY separation is induced by adding 188 µL of mass spec-grade water. After SP:SAMPLEPREP_SUMMARY vortexing for 20 s. The sample is centrifuged at 14,000 rpm for 2 min. The upper SP:SAMPLEPREP_SUMMARY organic phase is collected in two 300 µL aliquots. One is stored at -20ºC as a SP:SAMPLEPREP_SUMMARY backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are SP:SAMPLEPREP_SUMMARY resuspended using a mixture of methanol/toluene (9:1, v/v) (60 µL) containing SP:SAMPLEPREP_SUMMARY an internal standard [12-[[(cyclohexylamino)carbonyl]amino]-dodecanoic SP:SAMPLEPREP_SUMMARY acid (CUDA)] used as a quality control. #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:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Acquity UPLC CSH C18 CH:CHROMATOGRAPHY_TYPE Reversed phase #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE EI MS:MS_COMMENTS The quadrupole/time-of-flight (QTOF) mass spectrometers are operated with MS:MS_COMMENTS electrospray ionization (ESI) performing full scan in the mass range m/z MS:MS_COMMENTS 65–1700 in positive (Agilent 6530, equipped with a JetStreamSource) and MS:MS_COMMENTS negative (Agilent 6550, equipped with a dual JetStream Source) modes producing MS:MS_COMMENTS both unique and complementary spectra. Instrument parameters are as follows MS:MS_COMMENTS (positive mode) Gas Temp 325°C, Gas Flow 8 l/min, Nebulizer 35 psig, Sheath Gas MS:MS_COMMENTS 350°C, Sheath Gas Flow 11, Capillary Voltage 3500 V, Nozzle Voltage 1000V, MS:MS_COMMENTS Fragmentor 120V, Skimmer 65V. Data (both profile and centroid) are collected at MS:MS_COMMENTS a rate of 2 scans per second. In negative ion mode, Gas Temp 200°C, Gas Flow 14 MS:MS_COMMENTS l/min, Fragmentor 175V, with the other parameters identical to positive ion MS:MS_COMMENTS mode. For the 6530 QTOF, a reference solution generating ions of 121.050 and MS:MS_COMMENTS 922.007 m/z in positive mode and 119.036 and 966.0007 m/z in negative mode, and MS:MS_COMMENTS these are used for continuous mass correction. For the 6550, the reference MS:MS_COMMENTS solution is introduced via a dual spray ESI, with the same ions and continuous MS:MS_COMMENTS mass correction. Samples are injected (1.7 μl in positive mode and 5 μl in MS:MS_COMMENTS negative ion mode) with a needle wash for 20 seconds (wash solvent is MS:MS_COMMENTS isopropanol). The valve is switched back and forth during the run for washing; MS:MS_COMMENTS this has been shown to be essential for reducing carryover of less polar lipids. MS:ION_MODE POSITIVE MS:MS_RESULTS_FILE ST001640_AN002685_Results.txt UNITS:counts per second Has m/z:Yes Has RT:Yes RT units:Minutes #END