To get your data into Panorama, first create a folder.
- Hover over your project name in the menu bar below the Panorama icon and click on the New Subfolder icon shown in the image below.
- Select the Panorama option under Folder Type. This is the folder type that should be selected for all workflows supported by Skyline (SRM-MS, MS1 filtering or MS2 based projects).
- On the Users / Permissions page select one of the available options and click Next. You can also change permissions on a folder after it has been created.
- The next page (Configure Panorama Folder) asks you to choose the type of Targeted MS folder you would like to create. Panorama offers threechoices here.
- Choose the Experimental data option for folders that serve as a repository of Skyline documents, useful for collaborating, sharing and searching across multiple experiments.
- Choose Chromatogram library to store curated assays that can be used for designing and validating future experiments. Check Rank peptides within proteins by peak area if your data contains relative peptide expression for proteins.
- Choose the QC option for tracking performance of mass spec. instruments over time.
See the LabKey documentation for more information on creating and managing folders.