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MB Sample ID: SA200588
| Local Sample ID: | 89 |
| Subject ID: | SU002175 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 36-78 |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
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:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 89 | SA200588 | FL024355 | Case | Group |
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 | QTRAP |
| 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: | 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 |
