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

Abstract

<jats:p>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 (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://panoramaweb.org/public.url">https://panoramaweb.org/public.url</jats:ext-link>), 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.</jats:p>

A Proteomic Atlas of Senescence-Associated Secretomes for Aging Biomarker Development

“…Proteomic assays of SASP profiles are available on Panorama (https://panoramaweb.org/project/Schilling/SASP_Atlas_Buck/begin.view? ), a repository for targeted mass spectrometry assays generated in Skyline software (Sharma et al, 2014(Sharma et al, , 2018. All quantitative data is available for viewing and downloading on SASP Atlas (www.saspatlas.com).…”

“…DIA workflows are not limited by stochastic peptide MS/MS sampling biases introduced by more traditional data-dependent acquisition (DDA) mass spectrometry. In addition to our interactive, online database (SASP Atlas), we assembled and deposited proteomic panels of SASP factors on Panorama Web, a freely-available web-repository for targeted mass spectrometry assays (Sharma et al, 2014(Sharma et al, , 2018 as a resource for others to detect and quantify the SASP in mass spectrometric studies.…”

Targeted Approach to Distinguish and Determine Absolute Levels of GDF8 and GDF11 in Mouse Serum

“…The raw data are available at ProteomeXchange (PXD008395) and the entire PRM data set can be viewed as a Skyline document in Panorama Public via the following link: https://panoramaweb.org/BnW2U9.url. [ 8,12 ]…”

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

“…ProteomeXchange sets basic standards and minimum requirements for its members and fosters similar submission and dissemination policies. The main repositories of ProteomeXchange are PRIDE 127 , PeptideAtlas 128,129 (with its SRM component PASSEL 130 ), MassIVE 131 , jPOST 132 , iProX 133 , and Panorama Public 134 . Researchers are encouraged not only to deposit their final datasets in a ProteomeXchange repository, but also to consider downloading and examining previously downloaded and generated datasets to inform the generation of their own data.…”