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, filtering or MS2 based projects).
Panorama Folder Types
To begin working with Panorama: Create a new folder, choose Panorama
as the folder type, and on the Configure Panorama Folder
page, select one of the available configurations:
- Experimental data: A repository of Skyline documents, useful for collaborating, sharing and searching across multiple experiments.
- Multi-attribute method (MAM): An experimental data folder variant with additional reporting for multi-attribute method analyses.
- 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.
- 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
Multi-attribute Methods (MAM)
The Multi-attribute Methods folder is the same as the Experiment Data folder
with additional reports included as links in the Document Summary
- Post-translational Modification (PTM) Report: The PTM report shows the proportion for each peptide variant’s peak area across samples. Panorama automatically groups peptides with identical unmodified sequences, but a user can configure alternative groupings within the Skyline document, to group splice variants, for example.
- Peptide Map Report: The peptide map report shows the observed peptides in the MAM analysis, sorted by retention time. It compares the observed and expected masses, and the modifications for each peptide variant.
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
Additional documentation is available on the PanoramaWeb site