The first thing to do in your brand new project is to import Result Files.

There are many ways to open the dedicated tab:

• Right-click the Imported Search Results node, then click Import result File
• Right-click the project node, then click Import result File
• Right-click the project node, so that the project summary opens. Then click Import result File in this panel toolbar.

A new tab opens and displays the following panel.
Click on Select result files to browse and select them. The left side of the browsing window is meant for the directories. When you click on one of them, its content is shown on the main panel. Choose one or multiple files then click Ok.

Then configure the following parameters:

• Parameters
  • Software Engine: the software which generated your interrogation file
  • Instrument: mass-spectrometer used for sample analysis
  • Peaklist Software: the software used for the peaklist creation

• Decoy Parameters
  • Decoy Strategy: The type of decoy search which was performed.
    • “No Decoy Database”: if the search was performed against a target database only.
    • “Concatenated Decoy Database”: if target and decoy sequences were merged into a single database.
    • “Software Decoy”: if the “Decoy” sequences were generated on-the-fly by your search engine.
  • Protein Match Decoy Rule: for concatenated searches only. Select the rule to apply for the discrimination of target and decoy protein matches.

• Parser Parameters: according to your Software Engine, this will display some extra-parameters.
  • Mascot:
    • Ion Score Cutoff: peptide matches with a score lower than this value won't be imported
    • Subset Threshold: the percentage of score between a given protein match and the master protein match (superset). Protein matches with a relative score lower than

      Master_protein_score * (1-subset threshold)

      won't be imported.

  • Omssa:
    • User mod file: TODO
    • PTM Composition File: TODO

You can now click on “Start Import” to launch the check and the import tasks.

The server will check your files first, then the import itself will be launched automatically.

You can follow the current state of your tasks by clicking on the Tasks button at the bottom of the Project Tree panel.

It will open the Tasks Panel, listing all the tasks you've been running in Proline.

When a task is done, you are notified by a small message in the top of the screen, and you can see its status in the tasks window :

All the Result Files you have imported are listed in the Imported Search Results panel you can access by double-clicking the Imported Search Results node in your project tree.