After normalization, the Reporter Ions Quantifier node and the Precursor Ions Quantifier node calculate the grouped abundances for peptide groups and proteins. They use the following preprocessed abundances as a basis, when they are available:
- Ungrouped raw abundances, where no normalization and no scaling are applied
- Ungrouped normalized abundances
- Ungrouped scaled abundances (optionally also normalized)
The nodes calculate these as the average of the preprocessed sample abundances that belong to the same sample group. They calculate group abundances only when there is at least one sample group consisting of multiple samples.