Panorama: a targeted proteomics knowledge base

Abstract

Panorama is a web application for storing, sharing, analyzing, 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.

Figure 1

Skyline–Panorama dataflow. Users publish documents containing refined targeted methods from Skyline to a Panorama server, where they are stored in a relational database. Data uploaded to Panorama can be viewed, searched and analyzed in a web-browser interface. Documents published to Panorama as well as chromatogram libraries exported from library folders can be downloaded to view and use in Skyline.

Figure 2

Panorama web-browser interface showing the precursor list in a Skyline document. Clicking on one of the peptide sequences provides a more detailed view for the peptide that includes chromatograms for the precursors in all of the replicates. A graph showing the peak areas for the peptide measured in individual replicates is also displayed. Peak areas can be grouped by a replicate annotation, as shown above for the annotation “Condition” (Disease and Healthy). The source document can be downloaded via a DOWNLOAD link for viewing in Skyline.