When the application processes the data, it first extracts the raw quantification values during the processing step. For reporter ion quantification, these values are the intensities of the reporter peaks for each MSn spectrum. For precursor ion quantification, these values are the integrated peak areas or height. In the consensus workflow, the Reporter Ions Quantifier node or the Precursor Ions Quantifier, refers to the information generated during the analysis setup to determine which ratios to calculate for each file and which of these ratios to group by calculating an average ratio from them.
The ratio changes are currently color-coded. The area values are also color-coded, with the color ranging from yellow to red with increasing area.
The following figure shows the data distribution maps of the found ratio changes for the specified sample groups.
You can use the nth Fold Change Threshold parameters of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node to adjust the thresholds of the color highlighting in the Abundance and Abundance Ratios (log2) column of the Proteins page. For more information on these parameters and the color highlighting, refer to the Data Distributions node Help topic.
The display filters provide a means to filter data on the basis of the data distribution maps (for more information on display filters, see Filtering results data). The following figure gives an example of filtering for the proteins that have a fold change of at least four in at least five of the ratio groups present.