Quantification reporting using targeted mass spec assays with Panorama and Skyline

View Poster

Josh Eckels1; Marty Pradere1; Ron Dashwood1; Kristin Geddes2; Nicholas J Shulman3; Daniel S. Spellman2; Michael J MacCoss3; Brendan X MacLean3
1LabKey, San Diego, CA; 2Merck, West Point, PA; 3University of Washington, Seattle, WA


Panorama’s new reporting tools further extend its capabilities for managing absolute quantification results generated by targeted mass spectrometry assays. Panorama first added support for quantification assays in 2017, following closely on the Skyline targeted mass spec desktop application. This recent work reduces the number of external analysis tools required to analyze this data, as well the manual steps previously required to transfer data between applications. Additionally, Panorama’s user interface offers improved navigation, and the expanding data model can be leveraged to generate 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 interested group.


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 offers a growing library of reporting and analytics options. The underlying data is accessible via APIs and can be exported to Excel and other common formats.

Preliminary Data

Panorama now offers a variety of calibrated quantification reporting. In addition to the previously supported calibration curves and data tables, Panorama now calculates figures of merit and pharmacokinetics (PK) analysis, including charts. Panorama piggybacks on data embedded in the Skyline files for context, including expected concentrations, timepoints for sample creation, and more. Users can interact with the data, choosing starting and terminal time points and saving the results. Panorama will add additional preconfigured reports, including pharmacodynamic modeling. All of the data in Panorama is accessible through APIs, allowing users to create scripts in R and other programming languages to enable additional reports. By adding in this functionality, users are able to streamline processes that were once cumbersome and spread out across different software platforms. The impact will help the data processing bottleneck in many laboratories. As of January 2018, more than 250 labs are using a Panorama for free to manage targeted mass spectrometry assays on http://panoramaweb.org/, a server hosted by the University of Washington. Additionally, major pharmaceutical companies and other organizations have deployed their own in-house installations of Panorama.

Novel Aspect

Panorama now includes additional preconfigured quantification-based reports for targeted mass spec analysis, including figures of merit and pharmacokinetics.