Summary of Study ST001641

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 IDST001641
Study TitleRemodeling Lipids in the Transition from Chronic Liver Disease to Hepatocellular Carcinoma (Liver) - part II
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
DepartmentWest coast metabolomics center
LaboratoryFiehn lab
Last NameIsmail
First NameIsraa
Address451 health science drive, 95616 ,Davis, California, USA.
EmailIsraataher2015@gmail.com
Phone01 530 7613155
Submit Date2021-01-06
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

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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:SU001718
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 Sample Source
SA1512219 NT_085non tumor
SA15122210 NT_086non tumor
SA15122312 NT_088non tumor
SA1512248 NT_084non tumor
SA15122511 NT_087non tumor
SA1512266 NT_082non tumor
SA1512273 NT_079non tumor
SA1512284 NT_080non tumor
SA1512295 NT_081non tumor
SA15123013 NT_089non tumor
SA1512317 NT_083non tumor
SA15123214 NT_090non tumor
SA15123320 NT_096non tumor
SA15123421 NT_097non tumor
SA15123522 NT_098non tumor
SA15123623 NT_099non tumor
SA15123719 NT_095non tumor
SA15123818 NT_094non tumor
SA15123915 NT_091non tumor
SA15124016 NT_092non tumor
SA15124117 NT_093non tumor
SA1512422 NT_078non tumor
SA1512431 NT_077non tumor
SA1512448 T_061tumor
SA1512459 T_062tumor
SA15124610 T_063tumor
SA15124711 T_064tumor
SA1512487 T_060tumor
SA1512496 T_059tumor
SA1512502 T_055tumor
SA1512513 T_056tumor
SA1512524 T_057tumor
SA1512535 T_058tumor
SA15125412 T_065tumor
SA15125513 T_066tumor
SA15125620 T_073tumor
SA15125721 T_074tumor
SA15125822 T_075tumor
SA15125923 T_076tumor
SA15126019 T_072tumor
SA15126118 T_071tumor
SA15126214 T_067tumor
SA15126315 T_068tumor
SA15126416 T_069tumor
SA15126517 T_070tumor
SA1512661 T_054tumor
Showing results 1 to 46 of 46

Collection:

Collection ID:CO001711
Collection Summary:human liver samples were collected to compare tumor versus nontumor
Sample Type:Liver

Treatment:

Treatment ID:TR001731
Treatment Summary:comparison of tumor versus nontumor patients

Sample Preparation:

Sampleprep ID:SP001724
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.

Combined analysis:

Analysis ID AN002686
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 6550 QTOF
Ion Mode POSITIVE
Units counts per second

Chromatography:

Chromatography ID:CH001980
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:MS002485
Analysis ID:AN002686
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
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.
Ion Mode:POSITIVE
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