Customizable quality control metrics and notifications with Panorama, AutoQC, and Skyline

This poster was presented at the American Society for Mass Spectrometry (ASMS 2019) in Atlanta, Georgia.

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Josh Eckels1; Vagisha Sharma2; Marty Pradere1; Ankur Juneja1; Angelica Omaiye1; Cory Nathe1; Sweta Jewargikar1; Michael J MacCoss2; Brendan X MacLean2
1LabKey, San Diego, CA; 2University of Washington, Seattle, WA


Panorama’s newest quality control (QC) capabilities further extend its automated system suitability monitoring for targeted mass spectrometry assays. Panorama first added its QC folder type in 2015 in conjunction with AutoQC, a utility that monitors for newly-acquired system suitability runs targeting operator defined sets of peptide and small molecule standards. New runs are automatically analyzed using Skyline and imported into Panorama. Recent work greatly expands the metrics that can be monitored. Coupled with new types of statistical analyses and email alerts of outliers in newly acquired data, Panorama now offers an even more robust workflow. Developed as a module in the web-based data management platform, LabKey Server, free hosted projects are available to all interested groups.


Panorama now supports metrics that track values associated with the entire run such as statistics related to iRT regression, single replicate calibration and pressure traces, adding to its existing support for metrics associated with individual peptides and small molecules like retention time. Panorama includes a growing set of preconfigured metrics and lets users add custom metrics. Users can visualize their data using statistical process control plots including Levey-Jennings, moving range, and CUSUM. Administrators can customize thresholds for identifying outliers, or completely disable irrelevant or false-positive inducing metrics. Additionally, users can subscribe to email notifications summarizing the new data. Users can export plots and raw data in formats including PNG, PDF, Excel, or access them from other tools via APIs.


Panorama offers a growing collection of predefined QC metrics and has expanded beyond values associated with individual peptides and small molecules. In conjunction with enhancements to AutoQC and Skyline to provide more data that can be used to calculate metrics (an ongoing collaboration between the Skyline team and instrument vendors), users can perform much broader monitoring. Since Panorama now offers the ability to set up custom metrics, users can assess quality for data that is specific to their experimental design, such as monitoring the differences in retention time between different peptides to make sure they are not co- eluting. With the new ability to opt-in and opt-out of the full library of metrics and the ability to customize how outliers are defined, users have the tools needed to eliminate false positives and focus their system suitability checks on the most diagnostic data. By offering users the choice of either a daily summary of new data or the ability to be notified immediately of any outliers, the system is even more proactive in improving quality. With these additions to Panorama, users can further consolidate their workflows both to reduce the time spent on routine monitoring and to increases their efficacy. These enhancements will help reduce the data processing bottlenecks that occur in many laboratories. As of June 2019, more than 350 labs are using Panorama projects free of charge to manage targeted mass spectrometry assays on, a server hosted by the MacCoss lab at the University of Washington. Additionally, major pharmaceutical companies and other organizations have deployed their own in-house installations of Panorama.