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.
| Study ID | ST002091 |
| Study Title | Serum lipids are associated with nonalcoholic fatty liver disease: a pilot case-control study in Mexico |
| Study Summary | A 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 |
| Department | Biological Chemistry |
| Laboratory | UCLA Lipidomics |
| Last Name | Williams |
| First Name | Kevin |
| Address | BSRB 257, 615 Charles E. Young Drive S., Los Angeles, CA, 90095 |
| lipidomics@mednet.ucla.edu | |
| Phone | 3108254397 |
| Submit Date | 2022-02-09 |
| Num Groups | 2 |
| Total Subjects | 200 |
| Num Males | 52 |
| Num Females | 148 |
| Publications | PMID: 34629052 PMCID: PMC8504048 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | MS(Dir. Inf.) |
| Release Date | 2022-03-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 | QTRAP |
| MS instrument name | ABI Sciex 5500 QTrap |
| Ion Mode | POSITIVE |
| Units | nmol/ml |
MS:
| MS ID: | MS003180 |
| Analysis ID: | AN003415 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | QTRAP |
| 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 |
