For description on LCMS Quantitation you can first read the principles in this page : quantitionprinciple

To generate a XIC, right click on the Quantitation Node and select the “Extract Abundances” menu in the popup.

You can also copy an existing Experimental Design and generate a new XIC based on it: select the XIC you want to copy, right click and select “Clone & Extract Abundances…” menu.

To create the Design of your XIC, drag and drop the identifications from the right panel to the left panel.

If you drop an identification on the XIC Node, a Group and Sample parents' nodes will be automatically created.

You can also directly drop on a Group or Sample Node.

You can rename all the design nodes by different ways:

• by typing F2 when a node is selected
• by a long click on a node
• by the right button popup and the menu Rename

We recommend to rename at least the XIC node.

To be able to perform a XIC design, we need to know the source raw files.

Proline try to find in the database the corresponding Raw Files already registered. If a Raw file is not found, the icon shows a '!' and you can display the error by expanding the corresponding node. In this case, you will have to select the Raw File by yourself.

Note: To help you, you can display the peaklist tooltip by overriding the Identification Node in the Design Tree.

When the XIC Design is finished, click on the next button and select the parameters. See lcmslabelfreequantitationconfig to have more details about the different parameters.

Note: all the parameters are already set with default values.

When the XIC Design has been generated, it is added in the Quantitation Tree. You can display its properties, especially the configuration used, by the right mouse button popup:

You can delete a XIC Design, see how to delidf

You can rename a XIC Design, by clicking on “Rename…” in the popup menu.

You can export the XIC results, see how to export_an_identification_summary_a_xic_or_a_spectral_count