In order to create run Quantitation task, you must register your RAW files and corresponding MzDB files into Proline. To do so, click on the “Settings” button in the top bar of the Dataset Explorer application, and go to the “Raw File Registerer” tab.

• In the left grid, use the “Add Raw Files to Selection” button in order to select Raw Files
• In the right grid, use the “Add MzDB Files to Selection” button in order to select MzDB Files
• You can then make automatic pairs, based on file names, by clicking on the “Make Couples from RAW Files” button. This will automatically add matching files into the “Raw & MzDB Couples” grid.

When you're done, click on the “Launch Quantitation” button. The Task will appear in the tasks panel.

If you want to pair files whose names differ, you can proceed as follows :

• Select a file, either Raw or MzDB, in its grid,
• Click on the “Put in Couple” button,
• Select it in the “Raw & MzDB Couples” grid,
• Select the corresponding file of the other format (RAW or MzDB) in its grid,
• Click on its “Put in Couple” button.

After this, you must choose an Instrument Name and select the owner of the file in the users list.

Finally, click on “Register”. Note that this operation will fail if one of your raw file has already been registered.

Close the Settings Window.

Once you have registered your RAW Files, you must associate them to the Search Results you have imported into your project.

Double-click on the “Search Results” node in your project tree. The left grid lists the files you have imported. Select one in the grid, then use the right panel's form to search a registered Raw File (by filtering them on its name, its instrument name, its owner and/or its creation date) and select it in the results grid. Click on “OK” to associate it with the Result File you have selected in the left panel.

Once you have registered your Raw & MzDB Files and associated Raw Files to you Search Results, you are ready to create a Quantitation.

Double-click on the “Quantitations” node of your project tree to show you Quantitations table panel. It's empty if you haven't created any quantitation in this project yet. Click on the “New Quantitation” button to open the Quantitation Creation Panel.

Note that you can also open it by right-clicking on the Quantitation node or on the Project node itself.

The first tab of the Quantitation creation panel let you define a name, a description (optional), choose a type and a method.

TODO : details

Once you've made your choices, click on “Next”.

The Experimental design tab is where you define your Groups and Samples. By default, two groups are created and each one contains a sample.

You can create new groups by clicking on the “Add Group” button in the top bar of the tab. In each group, you can manage your sample by using the buttons in the left grid.

To add a Search Result to one of the samples of the group, select it in the left grid, and drag and drop a validated result set from your project's tree to the “Sample Analyses” grid

Once you have prepared all your group and samples, click on the “Next” button.

This tab let you set up you abundance extraction parameters.

TODO : Details

The purpose of this tab is to define the ratios between the groups your quantitation will rely on