GPF Importer Quick Reference

GPF Importer is a small application that automates the import of GPF or any peptide search data from Proteome Discoverer. This program imports the data with defaults that are appropriate for the Stellar MS, but the same result can be achieved through the Skyline File / Import / Peptide Search wizard.

• Peptide Search .pdResult File
  • Double click to open a file chooser for a .pdResult file. Since PD v3.1, a corresponding file with the .pdResultDetails extension must be present in the same folder.

• Fasta File

  • Double click to open a file chooser for a .fasta file.

• Output .sky File Name with Directory

  • Enter the full path to where you want the output .sky file to be. The folder must exist, and the extension of the file must be .sky for the red outline around the box to go away. Usually one can copy the path to a folder and paste here, and then type the desired .sky file.
    

• DIA Isolation Scheme

  • Select the isolation width used for your experiment. The chooser assumed that you used the Window Placement Optimization option in the Method Editor.
    
    

If for some reason, you didn't use Window Placement Optimization in the DIA method, it's possible to select a .raw file that has the DIA isolation scheme that you want to do. This is equivalent to using Skyline to Add an isolation scheme, and selecting Import.

The GPF creator does this for the pre-defined schemes, by creating a short 1 minute instrument method with a scheme, and acquiring the .raw file through Tune. You can find the template raw files if you can find the installed Skyline Tools directory by inspecting the Skyline Immediate Window when you launch a tool.

• Raw Files

  • Double click this box to select one or more .raw files that will be imported to the created .sky file after the spectral library is created from the .pdResult files.
    

• Import to Skyline

  • Click this button to start the import. As the import happens, the Skyline API logging text will print to the lower text box.
    

Once the import is finished (it can take minutes), the output skyline file will open, with all the data imported. You would be ready to create an assay with PRM Conductor next.