The Panorama Data Repository for Skyline Users.

Panorama is an open-source web-based data management system that was designed and developed for Skyline, a software tool for targeted mass spectrometry-based experiments. Panorama facilitates viewing, sharing, and disseminating targeted, quantitative results contained in Skyline documents. Panorama can be installed locally, or laboratories and organizations can sign-up for fully featured workspaces on the PanoramaWeb server (https://panoramaweb.org) hosted at the University of Washington. Workspaces on PanoramaWeb can be organized as needed by the owners and configured with fine-grained access controls to enable collaborative projects. To allow unlimited file storage Panorama projects can be set up to use cloud-backed storage such as Amazon Simple Storage Service (S3). In addition to storing and sharing Skyline results, Panorama together with Skyline is used for fully automated, longitudinal monitoring of LC-MS/MS system suitability. This is done with the Panorama AutoQC pipeline which automatically imports system suitability runs into a Skyline document as they are acquired. The document is uploaded to a Panorama server and several identification free metrics such as peak area, retention time etc. can be viewed as Levey-Jennings plots in a web-browser to track normal variation and quickly detect anomalies. Skyline documents and raw data on PanoramaWeb that are associated with research manuscripts can be submitted to the Panorama Public repository (https://panoramaweb.org/public.url) which is hosted on PanoramaWeb and is a member of the ProteomeXchange Consortium (http://www.proteomexchange.org/). Data on Panorama Public can be explored with a variety of graphs and annotated chromatographic peak views making it easy to evaluate quantitative results contained in the associated manuscripts. Access to data in the repository is managed as required, e.g. private access to reviewers during the manuscript review process and public access upon publication.