Absolute quantification using targeted mass spec assays with Panorama and Skyline

NICHOLAS SHULMAN1; JOSH ECKELS2; Vagisha Sharma1; Daniel S. Spellman3; Kristin Wildsmith4; Shadi Toghi Eshghi4; Jacob D Jaffe5; Michael J MacCoss1; Brendan MacLean1
1University of Washington, Seattle, WA; 2LabKey, San Diego, CA; 3Merck & Co., West Point, PA; 4Genentech, Inc, South San Francisco, CA; 5Broad Institute, Cambridge, MA


Panorama’s new support for absolute quantification further extend its capabilities for managing targeted mass spectrometry assays, including data management and visualization, and secure sharing with internal and external collaborators. The popular Skyline targeted mass spec desktop application added support for quantification assays in 2016, and this recent work closely integrates Panorama, ensuring the full analysis capabilities are available in both environments. Additionally, Panorama’s improved plotting and analysis tools facilitate downstream analytics in interactive charts or via custom scripts in languages like R. Developed as a module in the LabKey Server web-based 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 panoramaweb.org.


Skyline and Panorama combine to provide a workflow for managing and analyzing LCMS-based large and small molecule experiments. Absolute quantification is performed using either single-point or multiple-point calibration curves by spiking a heavy-labeled ‘standard’ analyte of known abundance. Users configure quantification within Skyline and publish their document to Panorama, which uses the same calculations to make the data available for reporting and visualization, in pre-defined reports like calibration curves.

Preliminary Data

Panorama now imports quantification data as configured in Skyline, loading it into its relational database. Panorama can also perform curve fit and other calculations using the same algorithms as Skyline, enabling interactivity with the data, as well as enabling custom analysis scripts in R and other programming languages to make further downstream use of the information. Additionally, new data views within Panorama generate figures of merit and assist users in performing quality control of their quantitative results. Panorama has also been recently optimized to better facilitate large and complex targeted mass spec datasets. As of January 2017, more than 200 labs are 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.

Novel Aspect

Skyline and Panorama now both support absolute quantification methods, simplifying analysis, assay data management, reporting, and collaboration.