When you select a PSM or a quantification spectrum for reporter ion quantification, the Quantification Channel Values chart displays the absolute intensity of the quantification values detected for the available quantification channels. When you select a protein or a peptide group, the chart displays the abundance of the item.
When you select a PSM or a quantification spectrum for precursor ion quantification, the Quantification Channel Values chart displays the area of the quantification values detected for the available quantification channels. When you select a protein or a peptide group, the chart displays the abundance of the item.
The chart shows the normalized abundances, if available, or the raw abundances. It can also display grouped abundances if they are available. Grouped abundances, which are the abundances of the sample groups defined on the Grouping and Quantification page of the study, appear as blue bars. Ungrouped abundances, which are the abundances of the samples defined on the Grouping and Quantification page of the study, appear as pastel-colored bars. Ungrouped abundances are ordered. When the results contain grouped and ungrouped abundances, you can use the shortcut menu commands in the chart to choose the data to display. The Show Legend command labels the ungrouped bars with the sample identifier. It also displays a legend for the colored bars.
The processing workflow must include a quantification node for this chart to appear in the results report.
Procedure
- Select the appropriate tab (Proteins, Peptide Groups, PSMs, or Quan Spectra) in the result file.
- Select the row of the protein, peptide group, PSM, or quantification spectrum that interests you.
- Choose View > Quan Channel Values, or select Quan Channel Values
.