Panorama: A Targeted Proteomics Knowledge Base

Abstract

Panorama is a web application for storing, sharing, analyzipanoramapaperdiagram2014ng, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington.

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Vagisha Sharma†, Josh Eckels‡, Greg K. Taylor‡, Nicholas J. Shulman†, Andrew B. Stergachis†, Shannon A. Joyner§, Ping Yan∥, Jeffrey R. Whiteaker∥, Goran N. Halusa⊥, Birgit Schilling#, Bradford W. Gibson#, Christopher M. Colangelo○, Amanda G. Paulovich∥, Steven A. Carr∇, Jacob D. Jaffe∇, Michael J. MacCoss†, and Brendan MacLean*†
† University of Washington, Seattle, Washington 98195, United States
‡ LabKey Software, San Diego, California 92101, United States
§ Carnegie Melon University, Pittsburgh, Pennsylvania 15213, United States
∥ Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
⊥ Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
# Buck Institute for Research on Aging, Novato, California 94945, United States
○ Yale University, New Haven, Connecticut 06520, United States
∇ The Broad Institute, Cambridge, Massachusetts 02142, United States

J. Proteome Res., 2014, 13 (9), pp 4205–4210
DOI: 10.1021/pr5006636
Publication Date (Web): August 7, 2014

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