Managing small molecule targeted mass spec assays using Skyline and Panorama

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Josh Eckels1; Vagisha Sharma2; Brian Pratt2; Tom Dunkley3; Kristin Wildsmith4; Cory Nathe1; Binal Patel1; Richard Johnson2; Jacob D. Jaffe5; Michael J. MacCoss2; Brendan MacLean2; 1LabKey Corp., Seattle, WA; 2University of Washington, Seattle, WA;  3 F. Hoffmann-La Roche Ltd, Basel, Switzerland; 4Genentech, Inc, San Francisco, CA; 5The Broad Institute, Cambridge, MA

Novel Aspect

Skyline and Panorama now both support small molecule data, simplifying quality control, assay data management, visualization, and collaboration.


Panorama’s new support for small molecule assays extends the features previously available for managing proteomics assays, including automated quality control workflows, data management and visualization, and secure sharing with internal and external collaborators. The popular Skyline targeted mass spec desktop application added support for small molecule assays in 2015, and this recent work closely integrates Panorama, bringing its newly improved support for monitoring multiple mass spec instruments’ performance at a glance. Additionally, Panorama adds capabilities to track revisions of the Skyline document for method building and similar uses. 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 workflow for managing and analyzing LCMS-based small molecule experiments. For QC scenarios, AutoQC, a utility suitable for installing on instrument control computers, monitors for newly acquired small molecule QC runs, runs Skyline without a user interface, and automatically publishes them to Panorama. There, key instrument performance metrics can be viewed for multiple instruments in a single dashboard. New QC plotting options reveal additional metrics and allow users to more easily visualize instrument performance. For experimental data, Panorama now tracks a full history of document versions, allowing users to see how they have changed over time.

Preliminary Data

As of February 2016, more than 140 labs are already using Panorama to manage targeted mass spectrometry assays on a server hosted by the University of Washington. Additionally, major pharmaceutical companies and other organizations have deployed their own installations of Panorama. The previously available proteomics support lets users organize, share, search, and analyze Skyline documents, track instrument performance in QC folders, and build curated observed chromatogram libraries. With the release of LabKey Server version 16.1, Panorama now supports small molecule assay data as well. Leading academic and commercial organizations use Panorama to collect, share, and analyze targeted mass spectrometry data, perform automated quality control, and have already adopted the new small molecule tracking. Multiple instrument configurations may be tracked using separate QC folders, available for viewing in a summary dashboard. Presenting both proteomics and small molecule data in an interactive, secure, web-based interface, gives all authorized users immediate access to both historic and just-acquired assays, regardless of type.