Andy Hoofnagle   Andy Hoofnagle, MD, Ph.D., is an Associate Professor in the Department of Laboratory Medicine at the University of Washington. His laboratory focuses on developing CLIA-certified assays for small molecules using mass spectrometry. They also investigate the function of high density lipoproteins in patients at increased risk for cardiovascular disease and the translation of proteomics technologies into the clinical laboratory.

Using Skyline for Lipidomics

Our interest in lipidomics is grounded in the likelihood that lipids are important mediators of disease via their influence on macrophages and endothelial cells. We have a special focus on the sphingolipids due to their fundamental role in cell signaling. Our laboratory has developed a novel single-step extraction method to quantify more than 100 lipids from high density lipoproteins. Current software solutions for peak integration and data handling are limited. We have identified a workaround in Skyline that allows for the rapid analysis of many samples simultaneously. The solution takes advantage of the excellent peak identification and integration capabilities in Skyline and has greatly simplified the workflow for lipidomics in our laboratory.

[PDF] [PowerPoint]

As of Skyline 3.1, native small molecule targeting has been added. (See Small Molecule Targets tutorial)


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