Laura Dubois is a research analyst at the Proteomics and Metabolomics Core Facility at Duke University in Durham, NC, directed by Dr. M. Arthur Moseley. She joined in 2008 as the third member of the facility, focusing on discovery (high resolution) and targeted (triple quadrupole) proteomics projects. She began using Skyline in early 2010 to analyze targeted LC-MS/MS data for a large clinical proteomics study in hepatitis C virus (HCV). Over the past few years, Laura has been heavily involved in the development of the facility’s metabolomics assays, including methods for polar metabolites, hydroxycholesterols, oxylipins, and lipidomics.

Expanding Skyline’s Capabilities to Small Molecule Data Analysis

Since Skyline’s public release in mid-2009, the continued developments have been focused on large molecule, proteomics applications. However, with studies in metabolomics gaining momentum, requests were being made to Skyline developers to broaden Skyline’s features to include method generation and data analysis tools for the investigation of small molecules. As with proteomics applications, the small molecule developments in Skyline make it a vendor-neutral tool that any mass spectrometrist can utilize for its ease-of-use, superior visual capabilities in data analysis, and readily available support. These enhancements simplify the metabolomics targeted method development process, and most importantly streamline data- and method-sharing across vendor platforms and laboratories, improving transparency in metabolomics studies. This presentation will showcase the workflow for performing targeted metabolomics analysis with Skyline, and discuss case studies where Skyline has aided our laboratory in the development of a variety of metabolomics assays.