Performing quality control on targeted proteomics assays using Skyline and Panorama

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Josh Eckels; Vagisha Sharma; Yuval Boss; Huilin Shi; Tom Dunkley; Kristin Wildsmith; Cory Nathe; Aaron Robinson; Richard Johnson; Jacob D. Jaffe; Michael J. MacCoss; Brendan MacLean


Novel Aspect

Skyline and Panorama now integrate with instruments to track assay performance, retain history and context, and visualize data.


Panorama’s new quality control (QC) folder type helps users efficiently identify and visualize assay performance issues and trends for targeted mass spectrometry data. Close integration with the popular Skyline targeted mass spec desktop application running on an instrument control computer allows reliable and automated data processing. Additionally, Panorama captures information about instrumentation, reagent, process, or other changes to help correlate with changes in instrument performance. Developed as a module in the LabKey Server data management platform, Panorama is freely available, open source and may be installed and managed by any laboratory or organization. Free, hosted Panorama projects are also available on


Skyline and Panorama combine to provide a robust QC workflow for LCMS instrumentation used in proteomics experiments. SkylineRunner runs Skyline without user interface for automated data processing, a mode suitable for QC workflows. SkylineRunner can be run on an instrument control computer to capture new QC runs automatically, and add them to an existing QC Skyline document, where the information is archived for later use and transferred to Panorama. Panorama retains a full history of QC run performance, and presents users with interactive plots for key metrics including retention time and peak area. Additionally, users can add information about changes including instrumentation, maintenance, and reagents, which are overlaid on the plots, providing a convenient way to correlate cause and effect.

Preliminary Data

As of January 2015, more than 90 labs are already using Panorama on a server hosted by the University of Washington. Additionally, major pharmaceutical companies and other organizations have deployed their own installations of Panorama. The existing experiment folder type lets users organize, share, search, and analyze Skyline documents. The chromatogram library folder type provides a mechanism for curating observed chromatograms, which can then be downloaded and used within Skyline to inform future assays. With the release of LabKey Server version 15.1, Panorama now supports quality control (QC) folders. Leading academic and commercial organizations use Panorama to collect, share, and analyze targeted mass spectrometry data, and have already adopted the new QC folder workflow. Integration of SkylineRunner with instruments from all of the major mass spectrometer vendors means that only a small number of standardized steps are now needed to configure a fully automated workflow to capture, retain, and visualize instrument performance based on a targeted assay. Multiple instrument configurations may be tracked using separate QC folders, allowing labs to monitor all of their equipment in a centralized location. Presenting the QC plots in an interactive, secure, web-based interface, gives all authorized users immediate access to both historic and just-acquired assays.