After classifying Quan Spectra, the Reporter Ions Quantifier node and the Precursor Ions Quantifier node calculate peptide group abundances for the different samples from their associated Quan Spectra. It calculates the abundance for a peptide group as a simple summation of its associated and used Quan Spectra abundances.
When the node calculates peptide group abundances, it creates the following columns:
- Peptide Quan Usage column on the PSMs page, which shows the PSMs that are used for calculating peptide group abundances. This column displays all PSMs, whether or not they are unique.
- Abundances column on the Peptide Groups page, which displays the peptide group abundances.
- Abundance Counts column on the Peptide Groups page, which displays the number of PSM abundances used for calculating the peptide group abundances.