Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline

Abstract

To address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers and readers immediate visual access to the data behind published conclusions, we present Panorama Public (https://panoramaweb.org/public.url), a repository of Skyline documents supporting published results. Panorama Public is built on Panorama, an open source data management system for mass spectrometry data processed with the Skyline targeted mass spectrometry environment. The Panorama web application facilitates viewing, sharing, and disseminating results contained in Skyline documents via a web-browser. Skyline users can easily upload their documents to a Panorama server and allow other researchers to explore uploaded results in the Panorama web-interface through a variety of familiar summary graphs as well as annotated views of the chromatographic peaks processed with Skyline. This makes Panorama ideal for sharing targeted, quantitative results contained in Skyline documents with collaborators, reviewers, and the larger proteomics community. The Panorama Public repository employs the full data visualization capabilities of Panorama which facilitates sharing results with reviewers during manuscript review.

Keywords: Bioinformatics software; Mass Spectrometry; Multiple reaction monitoring; Parallel reaction monitoring; Quantification; Targeted mass spectrometry; data repository; guidelines; panorama; skyline; software.

Fig. 1.

Workflow for submitting to Panorama Public. Steps 1 through 3 (data upload, annotation, and submission) are completed by researchers submitting their data to Panorama Public. To complete step 4 (copying to Panorama Public), administrators of Panorama Public make a copy of the data to Panorama Public and send a confirmation E-mail to the submitters once the data has been copied. If, during the submission process, submitters requested that their data on Panorama Public be kept private a read-only reviewer account is created and account details are included in the confirmation E-mail.

Fig. 2.

Step 3 of the submission workflow. Clicking on the “Submit” button (A) in the experiment description brings up a form that lets users generate a permanent link (B) to the data with a custom name. The permanent link can be included in manuscripts and given to journal editors during manuscript review. The link shown in the example is from a published data set (9) available on Panorama Public at https://panoramaweb.org/cptac_study9.url. The submitters may also request that their data on Panorama Public be kept private by checking a box in the form (C). Keeping data private may be suitable if it is associated with a manuscript under review. If this option is checked, the copy on Panorama Public is private with read-only access to submitters. An additional account is created with read-only access to the data, and account details are included in the confirmation E-mail sent to submitters after the data has been copied. These account details can be conveyed to journal editors at the time of manuscript submission and can be used by reviewers.

Fig. 3.

Copying data from a user project on PanoramaWeb to Panorama Public. Copy on Panorama Public is identical, both visually and in content, to the source folder in the user project, but may no longer be edited.

Fig. 4.

Chromatogram views on Panorama Public. Chromatograms are displayed in a tabular format with one row per replicate in which the peptide was measured. The first column displays the total precursor ion chromatograms followed by columns for fragment ion chromatograms. Chromatograms for isotopically labeled and unlabeled peptides are displayed in adjacent columns.