This panel is a summary of your experimental design, listing your biological groups, their samples and their technical replicates.

It also provides the “Profile Analysis” tool you need to launch in order to get Ratio informations and data to be exported.

This panel show all the data about the quantified proteins. By default, proteins are grouped, but you can undo it by clicking the icon circled in green in the previous screenshot. The view will then be:

This grid is also provided a filter tool, that you can use as follows:

Double-clicking a Protein will open its summary panel :

On this panel, you get an insight of all quantified peptides for this protein (double click on the peptide in the 'Quantified Peptides' table or expand directly the peptide panel).

You can click on the eye icon (circled in green) to access the Speclight viewer of this Peptide .

TODO: insert link to Speclight doc

This is the list of all quantified peptides.

• Click on a peptide to see its Master Quant Peptide Ions in the dedicated table below.
• Double-click on a peptide to open the panel for the feature corresponding to this peptide (see LC-MS Features).

Note that the peptide grid has got a filter tool too.

This panel offers two tabs to give you information about the LC-Ms maps of the experiment.

IMPORTANT: it is crucial to visit this graphics to manually control the processed map alignments. A bad alignment (showing many curve trends, or too large time deltas) will lead to quantitation errors. If you have the feeling that the alignment needs improvement, re-run the quantitation, tunning the Alignment Computation part of the LFQ Params tab (see how to create a quantitation).

On this chart, you can see all the delta time of each LC-MS map against the reference LC-MS map. The reference map is the one specified in the title of the chart. It corresponds to the x axis.

Click on one or many raw files to display their LC-Ms map features.

This panel lists all the features detected and processed by Proline. By clicking one of them, you can see the corresponding XIC on the right-side panel.

All the peaks are listed here, independently from the features they've been gathered to. Click on a Lc-Ms Map name to list all its peaks. By clicking on a peak you can see its XIC charts in the “XIC Viewer” at the bottom of the table, or you can double-click it to open the Xic Viewer in a new tab.

In order to see the ratio values, you have to launch the Profile Analysis from the Summary Panel.

This tab offers many panel to help you vizualise statistics about your quantitation.

The first one is a volcano chart of your Proteins based on their -Log10 T-Test P-Value over Log2 Ratio.

The Left grid shows a list of all the proteins, and if they are in the actual boudaries of the selection/exclusion tool.

The “AC Filters” let you select a color (by clicking on it) and enter an Accession Number (or a part of it) to highlight matching proteins on the chart).

The “Ratio” et “P-Value” let you define new boundaries for the protein selection / exclusion. It's show on the chart with black lines and gray points to show excluded proteins.

The second tab offers the same volcano chart for peptides, and you can highlight them with a sequence or ptm definition