Overcoming Key Challenges in Mass Spectrometry Data Management

Targeted mass spectrometry methods provide reproducible and quantitative analyses for a wide range of proteins and small molecules of interest. Mass spectrometrists need tools to help manage the data they generate, analyze it, and leverage their findings when designing new assays.

There are many approaches to mass spec, including Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), and Data Independent Acquisition (DIA/SWATH), each of which generates varying amounts of data for analysis. The variability, scale, and reproducibility requirements of these methods require a data management solution that is flexible, robust, and secure.

LabKey Server’s solution, Panorama, integrates closely with Skyline, a leading analysis application developed by the MacCoss lab at the University of Washington. With Panorama, LabKey supports the data management needs of mass spectrometrists by:

Centralizing Storage and Querying

LabKey Server acts as a shared data repository for Skyline documents, providing:

• A shared workspace for teams to collaborate on their analyses
• Tracking of multiple document versions of the same analysis
• Easy methods for sorting, filtering, querying, and accessing results via APIs
• Retrieval of previously analyzed data for reuse in Skyline

Tracking System Suitability

LabKey Server tracks system suitability with Panorama using:

• Longitudinal tracking of key metrics including retention time, peak area, and mass accuracy
• Automated import and analysis of newly acquired samples via integration with AutoQC Loader and Skyline
• Visualizations and statistical process controls like Levey-Jennings, CUSUM (cumulative sum), and moving range plots

Supporting Published Manuscripts

Using LabKey Server, Panorama Public meets the requirements for data submission with:

• Workflows for securing data prior to publication, then sharing it after review
• Compliance with ProteomeXchange requirements for submissions, including raw files
• Stable storage for supplemental data to accompany published manuscripts

LabKey Server helps research teams efficiently manage, analyze, and publish targeted mass spectrometry data at scale, maximizing its value. To learn more about using LabKey Server to manage targeted mass spectrometry data, check out the documentation library on the LabKey Support Portal or request a demo. LabKey’s lead for Panorama, Josh Eckels, will be in Atlanta for the Annual Conference of the American Society for Mass Spectrometry.