Create a folder in Panorama

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.
  • Give the new folder a Name.
  • 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 several choices 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 the Multi-attribute method (MAM) option for an Experimental data folder including additional reporting for multi-attribute method analyses.
    • 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 Quality control (QC) option for tracking performance of mass spec. instruments over time.
  • Click Finish.

Changing the folder type

If you forget to select "Panorama" as the folder type option when creating a new folder, the folder will not be recognized by Skyline as a folder where it can upload Skyline documents. The folder will also not have the layout that you expect to see in a "Panorama" folder. For example, the Raw Data tab where you can upload raw files will not be available. You can change the folder type by following these steps:
  • Click the gear icon in the top right corner and select Folder and then Management
  • In the Folder Management interface select the Folder Type tab as show in the image below
  • Select Panorama as the folder type option and click the Update Folder button

See the LabKey documentation for more information: