The lipidomic approach in the laboratory of Yan Xu deals with understanding, at the molecular level, the mechanism of development of ovarian, breast, prostate, and other malignancies. These include developing effective diagnostic and prognostic biomarkers for these diseases and novel therapeutic targets and methods to treat them. The efforts of the Xu laboratory will focus on

• investigating the role and signaling mechanisms of bioactive lipip molecules, lysophosphatidic acid (LPA), lysophosphatidylcholine (LPC), and sphingosylphosphorylcholine (SPC) and their receptors in cancer and other diseases.
• determining the structure-function relationship of the OGR1-subfamily receptors and establish molecular models of these receptors for drug development.
• determining the physiological roles and functions of OGR1-subfamily receptors using mouse knockout models.

Xu's studies have already shown that a group of lysophospholipids can detect colorectal cancer with high sensitivity and specificity. Confirmation and expansion of these studies will be pivotally important for the critical evaluation of the clinical usage of these biomarkers. Lidipomics is a relatively new field and the inclusion of this analysis in Cancer Care Engineering OMIC analyses represents a novel addition and provides great promise for increasing the value of the predictive statistical models that will be generated.

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Instruments

The lipidomics workflow uses the Applied Biosystems API 4000 QTRAP, a Triple Quadrupole LC/MS/MS System. The QTRAP is a robust, highly sensitive system that provides advanced structure identification to accurately detect the masses of both molecular and product ions.

See sample preparation protocol and instrument setup for detailed descriptions of the sample processing methodologies.

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Analysis Workflow

The Applied Biosystems API 4000 QTRAP generateds WIFF files during instrument sample analysis (about 30 samples at a time), which are converted converted to Excel spreadsheets and then to CSV files containing the raw lipid data used as input for analysis. The dataset workflow is shown here.

Internal standard curves(IS) are established for the lipidomics analysis and applied to the raw data intensity values generated by the AB-4000. The ratio of the (raw) lipid peak area to the IS peak area is used to compute the final concentrations of the specific lipids under investigation: S1P, 16:0 LPA, 18:2 LPA, 18:1 LPA,18:0 LPA, 20:4 LPA, 22:6 LPA, 16:0 LPI, 18:0 LPI, 20:0 LPI, AA, 15-HETE, PGE2. See these example computations for ion detection.

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Datasets

The Applied Biosystems API 4000 QTRAP generates ".WIFF" files containing the lipid analysis data. The instrument-generated WIFF dataset is converted to an Excel spreadsheet, and the data in the XLS dataset is pre-processed using standard curves computed specifically for the instrument setup and analysis conditions. The raw and pre-processed XLS files will also be used by the Cancer Care Engineering statistical modeling group for integrative mathematical modeling

Here are sample data files generated by Zhenwen Zhou of the lipidomics research laboratory for the lipidomics workflow which will be used for the Cancer Care Engineering plasma sample analysis.

• Excel spreadsheet dataset for 10 samples and compounds SPC, L-PAF, 14-0 LPC, 18:2 LPC, etc.
• converted comma-separated-variable dataset for the Excel spreadsheet