An Open Source Proteomics and Metabolomics Visualization and Development Tool for Quantitative Mass Spectrometry Experiments

Session ID#: 9561

Session Description:
Proteomics and metabolomics are becoming desired analytical tools for understanding biological interactions and biochemical responses in isolated organisms and mixed communities in marine systems. These high-throughput technologies allow us to monitor and compare thousands of biological molecules, providing an important approach for oceanographers as we work towards predictive understanding of biological processes in the marine environment.  Although highly desirable, the bioinformatics can be daunting, creating a barrier for investigators to get started in the field of quantitative or discovery-driven proteomics.  We will discuss how to develop and analyze proteomic experiments in organisms using the software Skyline.  Skyline is a freely-available, open source Windows client application for visualizing and analyzing targeted proteomics data, building targeted proteomic method files, and quantifying MS1 precursor ions for comparison.  The Skyline platform is a community open-source collaboration integrated with a wide variety of external software tools with worldwide support and a current user base of >5,000 investigators.  Skyline developers are currently building visualization tools for quantitative metabolomics.  This tutorial will walk potential users through the Skyline platform, demonstrating its abilities and answering questions. Computational and statistical aspects of quantitative mass spectrometry proteomics will be discussed with reference to discovery and targeted proteomics.
Moderator:  Steven G Ackleson, S A Ocean Services, Falls Church, VA, United States
Primary Presenter:  Brook L Nunn, University of Washington, Department of Genome Sciences, Seattle, United States
Presenter:  Emma Timmins-Schiffman, University of Washington, Department of Genome Sciences, Seattle, WA, United States
Index Terms:

1910 Data assimilation, integration and fusion [INFORMATICS]
1976 Software tools and services [INFORMATICS]
4840 Microbiology and microbial ecology [OCEANOGRAPHY: BIOLOGICAL AND CHEMICAL]
  • CT - Chemical Tracers, DOM and Trace Metals
  • ME - Marine Ecosystems