Proline

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The first thing to do in your brand new project is to import Result Files. To do so, Click on the “Import Result File” Button, in the toolbar of the project overview window or via a “right-click” on the Project node of the tree

You should then see this panel appear :

It allows you to select Result Files and set up following parameters for the import process :

• 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 : TODO
  • Protein Match Decoy Rule : TODO

• Parser Parameters : according to your Software Engine, this will display some extra-parameters.
  • Mascot :
    • Ion Score Cutoff : TODO
    • Subset Threshold : TODO
    • Mascot Server URL : TODO
  • Omssa :
    • User mod file : TODO
    • PTM Composition File : TODO

• Check Files before Import : let this checked to ensure that your files contain no errors. The server will perform a check operation before launching the import.

In order to add files to your import selection, click on “Select Result File” to open the File Browser that will let you choose one or many result files to import :

The left side let you browse the directories, and when you click on one of them, its content is shown on the main panel. Choose one or multiple files then click “Ok”.

Back to the “Import Result File” window, you should now see your selection appear in the grid. Choose the instrument and the peaklist software corresponding to your files, and then select a “Decoy Strategy”. 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 small cake in the bottom right corner of the desktop screen. It opens a small grid where you can see all your tasks.

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 :

Once your Result Files have been imported, you can use them to create a new Identification Dataset. Click on the “Identification Trees” element in the tree, on the left side of the window. The grid which just appeared is meant to list all your datasets. For now, you can only see the “Trash”, but you can create a new one by clicking on the “New Dataset” button.

You should now see a window asking to choose a source of data for your new Dataset. Choosing “Result Summary” will let you build a new dataset from one or more existing validated identification dataset. Il will duplicate them into a new Dataset without their validation data. Choosing “Result Set” allows you to build a new dataset from both Result Files you have imported and existing identification datasets, whether they have been validated or not. For now, assuming you are creating your first identification dataset, you should choose the “Result Set” option. On the two-tabbed panel, go to the “Result Sets” tabs in order to see the list of the files you have imported.

To add one or many files to your selection, select them in the grid (you can use the Ctrl and the Shift keys to make a multiple selection), then click on “Add to Selection” on the bottom of the window. You can also double click on one file to quickly add it to the selection. To remove any file from the selection, just select them and click on “Remove selected Items”. Type a name for your dataset then click on “Create”. The creation of your identification dataset takes the following form : - An “Aggreagation” Dataset Node is created. It takes the name that you provided during the creation. - One “Identification” Dataset Node is created for each one of the Result Files you have selected. They take the name of the Result File.

Once your Identification Dataset has been created, you can see it on the tree, in the left side of the window.

The panel of the Aggregation Node shows a list of your Identification fractions (corresponding to each imported file) and, after the validation process, it will display the Merged Result Summary infos.