There are 2 ways to open the Quantitation Creation form:

• Right-click on the Quantitations node of the project tree, then click New Label Free Quantitation in its menu
• Double-click on this node to open the Quantitations table panel. It's empty if you haven't created any quantitation in this project yet. Click the New Label Free Quantitation button to open the creation form.

The first tab of the creation panel, entitled Information, let you define a name and an optional description for your quantitation. Type and method are disabled since the label free base on abundance extraction is the only combination available yet.

Click on Next to go to the next step.

The Experimental design tab is where you define your Groups and Samples.

The simplest way to create biological groups (e.g. representing biological conditions) is to drag the validated nodes from the project tree and drop them in the dedicated zone. Drag/drop the nodes one by one.

In the example below, two groups are created this way:

For more complex experimental design, click on Add New Sample to add a sample (e.g. biological replicate) to your group. Enter the name of the sample, then drag/drop the corresponding node to the right panel to add it.

In most of the cases, the definitions go as following:

• biological group = biological condition
• biological sample = biological replicate
• sample analysis = technical replicate

However, these definitions are not strict and you can use and adapt the hierarchy to fit your needs. Tooltips are available to help you remind it (place your mouse over the terms to see them).

Once you have prepared all your groups and samples, click on the Next button.

This tab let you set up you abundance extraction parameters.
Depending on your choices, some parameters will become available/unavailable (e.g. clustering parameters are visible only when extracting from MS/MS events).

Tooltips are available to help you understand each parameter.
See more details on these parameters.
See more details on the quantitation process.

Tip: If you are creating a quantition that you've already done in the past (i.e. using the same files), select the Use previous peakel detection to go much faster. It will skip the long step of peakel detection and use what was previously found instead.

Click on Next to go to the last tab.

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

You can define the ratios:

• one by one: specify the numerator and denominator in the Add single ratio section
• in batch: automatically generate the ratio of each group against a reference group. Use the first section to do it.

Click the “double arrow” icon to invert numerator and denominator in a ratio.

When you're done, just press the Launch Quantitation button. You will be noticed when the task is finished