Summary of Study ST002091

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 PR001327. The data can be accessed directly via it's Project DOI: 10.21228/M8641H 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 IDST002091
Study TitleSerum lipids are associated with nonalcoholic fatty liver disease: a pilot case-control study in Mexico
Study SummaryA nested case-control study was conducted with a sample of 98 NAFLD cases and 100 healthy controls who are participating in an on-going, longitudinal study in Mexico. NAFLD cases were clinically confirmed using elevated liver enzyme tests and liver ultrasound or liver ultrasound elastography, after excluding alcohol abuse, and 100 controls were identified as having at least two consecutive normal alanine aminotransferase (ALT) and aspartate aminotransferase (AST) (< 40 U/L) results in a 6-month period, and a normal liver ultrasound elastography result in January 2018. Samples were analyzed on the Sciex Lipidyzer Platform and quantified with normalization to serum volume. As many as 1100 lipid species can be identified using the Lipidyzer targeted multiple-reaction monitoring list. The association between serum lipids and NAFLD was investigated using analysis of covariance, random forest analysis, and by generating receiver operator characteristic (ROC) curves.
Institute
University of California, Los Angeles
DepartmentBiological Chemistry
LaboratoryUCLA Lipidomics
Last NameWilliams
First NameKevin
AddressBSRB 257, 615 Charles E. Young Drive S., Los Angeles, CA, 90095
Emaillipidomics@mednet.ucla.edu
Phone3108254397
Submit Date2022-02-09
Num Groups2
Total Subjects200
Num Males52
Num Females148
PublicationsPMID: 34629052 PMCID: PMC8504048
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailMS(Dir. Inf.)
Release Date2022-03-18
Release Version1
Kevin Williams Kevin Williams
https://dx.doi.org/10.21228/M8641H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001327
Project DOI:doi: 10.21228/M8641H
Project Title:Serum lipids are associated with nonalcoholic fatty liver disease: a pilot case-control study in Mexico
Project Type:Lipidomics
Project Summary:Lipidomics analysis of 100 serum samples from NAFLD patients with a matched control group.
Institute:University of California, Los Angeles
Department:Biological Chemistry
Laboratory:UCLA Lipidomics Lab
Last Name:Williams
First Name:Kevin
Address:BSRB 257, 615 Charles E. Young Drive S., Los Angeles, CA, 90095
Email:lipidomics@mednet.ucla.edu
Phone:3108254397
Publications:PMID: 34629052 PMCID: PMC8504048

Subject:

Subject ID:SU002175
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:36-78
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Group
SA20058175Case
SA20058276Case
SA20058374Case
SA20058473Case
SA20058572Case
SA200586157Case
SA200587153Case
SA20058889Case
SA200589148Case
SA20059088Case
SA200591152Case
SA20059271Case
SA200593155Case
SA20059470Case
SA200595166Case
SA20059661Case
SA200597167Case
SA20059857Case
SA20059956Case
SA20060062Case
SA20060165Case
SA200602161Case
SA20060368Case
SA200604162Case
SA20060566Case
SA200606145Case
SA20060795Case
SA200608116Case
SA200609118Case
SA200610115Case
SA200611114Case
SA200612113Case
SA200613134Case
SA200614120Case
SA200615126Case
SA200616131Case
SA200617132Case
SA200618122Case
SA200619110Case
SA200620138Case
SA20062199Case
SA200622100Case
SA20062398Case
SA200624144Case
SA20062596Case
SA2006261Case
SA200627142Case
SA200628139Case
SA200629106Case
SA200630105Case
SA200631141Case
SA200632168Case
SA200633163Case
SA200634194Case
SA20063531Case
SA20063654Case
SA200637183Case
SA20063827Case
SA200639195Case
SA20064010Case
SA200641191Case
SA20064234Case
SA20064333Case
SA200644180Case
SA200645184Case
SA200646185Case
SA20064719Case
SA20064818Case
SA200649190Case
SA20065015Case
SA200651189Case
SA200652192Case
SA200653186Case
SA200654187Case
SA200655188Case
SA20065621Case
SA20065735Case
SA200658196Case
SA20065944Case
SA200660174Case
SA200661197Case
SA200662170Case
SA200663200Case
SA20066446Case
SA20066548Case
SA2006662Case
SA200667172Case
SA20066842Case
SA20066951Case
SA200670179Case
SA200671169Case
SA20067253Case
SA200673198Case
SA200674171Case
SA20067537Case
SA2006766Case
SA200677178Case
SA200678177Case
SA200679199Case
SA200680129Control
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Collection:

Collection ID:CO002168
Collection Summary:A convenience sample of 98 NAFLD cases and 100 healthy controls aged 36 to 78 years, who are long-term participants in the HWCS was used for the current pilot study. The inclusion criteria for this study were having a hepatologist-confirmed diagnosis of NAFLD for the cases, and a history of normal ALT and AST results (< 40 U/L) plus a normal ultrasound elastography result for the controls. Liver enzymes (ALT, AST), total cholesterol, high-density lipoprotein (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides, glucose, body mass index (BMI), waist circumference, and blood pressure were measured. Participants reported fasting for ≥12 h at blood draw. Serum samples that were collected during 2011–2013 and stored at − 70 °C, as well as self-reported data and laboratory results that were obtained during the same time period, were used for the cases and controls. https://pubmed.ncbi.nlm.nih.gov/34629052/
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002187
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP002181
Sampleprep Summary:Bligh and Dyer lipid extraction for subsequent lipidomics analysis using the Sciex Lipidyzer Mass Spectrometry Platform (Bligh and Dyer, 1959). The protocol is a modified version of the Serum Extraction Protocol published in the Lipidyzer Platform user guide (Sciex, 2016). For internal standard preparation, see Chemical preparations of the Lipidyzer Platform user guide (Sciex, 2016) and (Ubhi, 2018). For more details, check the following published protocol: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753944/

Combined analysis:

Analysis ID AN003415
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system Sciex 5500
Column none
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode POSITIVE
Units nmol/ml

Chromatography:

Chromatography ID:CH002526
Chromatography Summary:For each sample, there are 2 .mzML files.
Instrument Name:Sciex 5500
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS003180
Analysis ID:AN003415
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Hardware/System Setup: The Lipidyzer platform hardware has been described previously. (10) The Turbo V source is outfitted with a 65 μm ESI Electrode and the transfer line is plumbed with 50 μm ID PEEKsil tubing from the Lipidyzer installation kit. For the SLA application method, a 100 μL loop was installed. SLA Overview: The Shotgun Lipidomics Assistant (SLA) oversees three processes in the DMS lipidomics workflow: (1) analyzing DMS tuning data to update methods utilizing the DMS, (2) analyzing QC/suitability test data to measure relative lipid standard response, and (3) analyzing DMS lipidomics data files to yield processed quantitative results. This third process is subdivided into three parts: (1) extracting data from Analyst data files, (2) merging extracted data with the sample map and performing normalization, and (3) creating plots and data sheets of the class total and triacylglycerol data. These five processes are carried out on separate tabs within the SLA GUI. We will describe each of these five processes and the computations performed in detail below. While the LWM scripted the creation of Analyst sample batches and performed data analysis for these three processes, our workflow allows the user to setup the batches manually in Analyst and performs the analysis on the resulting data. This manual batch creation step requires a minimal amount of user time and gives the user flexibility in performing tuning, QC/suitability tests, and analyzing experimental data. The first step of analysis within each of the three primary processes is the conversion of the WIFF files to mzML format using Proteowizard’s MSconvertGUI application. (11) The SLA reads the resulting mzML files utilizing the pyOpenMS package (12) and converts the data into readable data tables for further data processing. Please refer to the following publication for more details: https://pubmed.ncbi.nlm.nih.gov/34637296/
Ion Mode:POSITIVE
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