Panorama is a freely available, open-source web server database application for targeted proteomics assays that integrates into a Skyline proteomics workflow. The LabKey Panorama module supports management of targetted mass spectrometry data and integration with Skyline workflows (SRM-MS, MS1 filtering or MS2 based projects). To begin working with Panorama: Create a new folder, choose Panorama as the folder type, and select one of the three available configurations:

• Experimental data: A repository of Skyline documents, useful for collaborating, sharing and searching across multiple experiments.
• Chromatogram library: Curated precursor and product ion expression data for use in designing and validating future experiments. Check Rank peptides within proteins by peak area if your data contains relative peptide expression for proteins.
• QC: Quality control metrics of reagents and instruments.

Additional documentation is available on the PanoramaWeb site.

Experimental Data

The Sharing Skyline Documents Tutorial on the PanoramaWeb site provides an introduction to using Panorama and covers the following areas:

• Requesting a project on panoramaweb.org
• Data organization and folder management in Panorama
• Publishing Skyline documents to Panorama
• Data display options and searching results uploaded to Panorama
• Providing access to collaborators and other groups
• Panorama: Heat Maps
• Panorama Document Revision Tracking

Chromatogram Library

In the Panorama Chromatogram Libraries Tutorial you will go through the steps of creating a library folder in Panorama for storing curated, targeted results.

• Build a chromatogram library in Panorama
• Use it in Skyline to select peptides and product ions to measure in a new experimental setting
• Compare library chromatograms with new data to validate peptide indentifications.

Panorama QC Folder

• Panorama QC Dashboard: Overview of the Panorama QC Folder
• Panorama QC Plots: Panorama QC Plots