Summary of Study ST001640

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001049. The data can be accessed directly via it's Project DOI: 10.21228/M83Q4K This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001640
Study TitleRemodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular Carcinoma (Blood) - part I
Study SummaryComparing 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
Last NameIsmail
First NameIsraa
Address451 Health Sciences Drive, Room 1313, Davis, CA, 95616, USA
EmailIsraataher2015@gmail.com
Phone01 530 7613155
Submit Date2021-01-04
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS
Release Date2021-01-25
Release Version1
Israa Ismail Israa Ismail
https://dx.doi.org/10.21228/M83Q4K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001049
Project DOI:doi: 10.21228/M83Q4K
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:University of California, Davis
Department:West Coast Metabolomics Center
Last Name:Ismail
First Name:Israa
Address:451 Health Sciences Drive, Room 1313, Davis, CA, 95616, USA
Email:Israataher2015@gmail.com
Phone:01 530 7613155
Funding Source:This research was funded by the U.S. National Institutes of Health, U2C ES030158 (to O.F.) and the Egyptian Ministry of Higher Education (to I.T.I).

Subject:

Subject ID:SU001717
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA15116821P_021CLD
SA15116922P_022CLD
SA15117020P_020CLD
SA15117118P_018CLD
SA15117217P_017CLD
SA15117323P_023CLD
SA15117419P_019CLD
SA15117524P_024CLD
SA15117629P_029CLD
SA15117730P_030CLD
SA15117828P_028CLD
SA15117926P_026CLD
SA15118025P_025CLD
SA15118116P_016CLD
SA15118227P_027CLD
SA1511831P_001Control
SA1511846P_006Control
SA1511855P_005Control
SA1511863P_003Control
SA15118715P_015Control
SA1511882P_002Control
SA1511897P_007Control
SA1511904P_004Control
SA1511918P_008Control
SA15119214P_014Control
SA15119313P_013Control
SA15119412P_012Control
SA15119510P_010Control
SA1511969P_009Control
SA15119711P_011Control
SA15119847P_047HCC
SA15119946P_046HCC
SA15120045P_045HCC
SA15120148P_048HCC
SA15120244P_044HCC
SA15120352P_052HCC
SA15120443P_043HCC
SA15120553P_053HCC
SA15120651P_051HCC
SA15120750P_050HCC
SA15120849P_049HCC
SA15120935P_035HCC
SA15121034P_034HCC
SA15121133P_033HCC
SA15121232P_032HCC
SA15121331P_031HCC
SA15121436P_036HCC
SA15121537P_037HCC
SA15121641P_041HCC
SA15121740P_040HCC
SA15121839P_039HCC
SA15121938P_038HCC
SA15122042P_042HCC
Showing results 1 to 53 of 53

Collection:

Collection ID:CO001710
Collection Summary:Samples of both plasma and liver were collected from healthy patients and patients with chronic liver diseases.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001730
Treatment Summary:Healthy patients (control) versus CLD and HCC for plasma.

Sample Preparation:

Sampleprep ID:SP001723
Sampleprep Summary:Extraction of plasma lipids is based on the “Maytash'' method [1] which was subsequently modified. Extraction is carried out using a bi-phasic solvent system of cold methanol, methyl tert-butyl ether (MTBE), and water. In more detail, cold methanol (225 µL) containing a mixture of odd chain and deuterated lipid internal standards [lysoPE(17:1), lysoPC(17:0), PC(12:0/13:0), PE(17:0/17:0), PG(17:0/17:0), sphingosine (d17:1), d7-cholesterol, SM(17:0), C17 ceramide, d3-palmitic acid, MG(17:0/0:0/0:0), DG(18:1/2:0/0:0), DG(12:0/12:0/0:0), and d5-TG(17:0/17:1/17:0)] is added to a 20 µL sample aliquot, which is placed into a 1.5 mL Eppendorf tube, and the tube is vortexed for 10 s. Then, 750 µL of cold MTBE containing CE(22:1) (internal standard) are added, followed by vortexing for 10 s. and shaking for 6 min. at 4ºC. Phase separation is induced by adding 188 µL of mass spec-grade water. After vortexing for 20 s. The sample is centrifuged at 14,000 rpm for 2 min. The upper organic phase is collected in two 300 µL aliquots. One is stored at -20ºC as a backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are resuspended using a mixture of methanol/toluene (9:1, v/v) (60 µL) containing an internal standard [12-​[[(cyclohexylamino)carbonyl]amino]-​dodecanoic acid (CUDA)] used as a quality control.

Combined analysis:

Analysis ID AN002685
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent
Column Waters ACQUITY UPLC CSH C18
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6530 QTOF
Ion Mode POSITIVE
Units counts per second

Chromatography:

Chromatography ID:CH001979
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.
Instrument Name:Agilent
Column Name:Waters ACQUITY UPLC CSH C18
Column Temperature:65
Flow Gradient: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).
Flow Rate:0.6 mL/min
Solvent A:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS002484
Analysis ID:AN002685
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The quadrupole/time-of-flight (QTOF) mass spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 65–1700 in positive (Agilent 6530, equipped with a JetStreamSource) and negative (Agilent 6550, equipped with a dual JetStream Source) modes producing both unique and complementary spectra. Instrument parameters are as follows (positive mode) Gas Temp 325°C, Gas Flow 8 l/min, Nebulizer 35 psig, Sheath Gas 350°C, Sheath Gas Flow 11, Capillary Voltage 3500 V, Nozzle Voltage 1000V, Fragmentor 120V, Skimmer 65V. Data (both profile and centroid) are collected at a rate of 2 scans per second. In negative ion mode, Gas Temp 200°C, Gas Flow 14 l/min, Fragmentor 175V, with the other parameters identical to positive ion mode. For the 6530 QTOF, a reference solution generating ions of 121.050 and 922.007 m/z in positive mode and 119.036 and 966.0007 m/z in negative mode, and these are used for continuous mass correction. For the 6550, the reference solution is introduced via a dual spray ESI, with the same ions and continuous mass correction. Samples are injected (1.7 μl in positive mode and 5 μl in negative ion mode) with a needle wash for 20 seconds (wash solvent is isopropanol). The valve is switched back and forth during the run for washing; this has been shown to be essential for reducing carryover of less polar lipids.
Ion Mode:POSITIVE
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