Proline

To display a XIC, right click on the selected XIC node in the Quantitation tree, and select “Display Abundances”, and then the level you want to display:

By clicking on “Display Abundances” / “Protein Sets”, you can see all quantified protein sets. For each quantified protein set, you can see below all peptides linked to the selected protein set and peptides Ions linked to the selected peptide. For each peptide Ion, you can see the different features and the graph of the peakels in each quantitation channel.

The overview is based by default on the abundances values. (Note: if you sort on the overview column, the sort is based on max(value-mean(values))/mean(values). So, you will obtain the most homogenous and confident rows first)

For each quantitation channel, are displayed:

- the raw abundance

- the peptide match count (by default)

- the abundance (by default)

- the selection level

By clicking on the “Column Display Button” , you can choose the information you want to display or change the overview.

To display the identification protein Set view, click right on the selected protein Set and select “Display Identification Protein Sets” menu in the popup.

You can also display the identification summary result from the popup menu in the quantitation tree:

A graph allows you to see the variations of the abundance (or raw abundance) of a peptide in the different quantitation channels:

You can see the different features in the different quantitation channels and the graph of the peakels:

By clicking on you can display either:

- the peaks of isostope 0 in all quantitation channels

- all isotopes for the selected quantitation channel:

By clicking on you can see the chromatograms of the features and their first time scan and last time scan in mzScope. For more details see the mzScope section.

By clicking on “Display Abundances“ / “Peptides”, you can see:

- identified and quantified Peptides

- non identified but quantified peptides

- identified but not quantified peptides (linked to a quantified protein)

By clicking on “Display Abundances” / “Peptides Ions”, you can see:

- all identified and quantified Peptides Ions

- non identified but quantified peptides Ions

By clicking on “Exp. Design > Parameters”, you can see the experimental design and the parameters of the selected XIC.

If you have launched the refinement of the protein sets abundances on the XIC, you can also display the refinement parameters.

By clicking on “Exp. Design > Map Alignment”, you can see the map of the variation of the alignement of the maps compared to the map alignment of the selected XIC. You can also calculate the predicted time in a map from an elution time in another map.