Normalizing peptide groups and protein abundances - Proteome Discoverer Software - Normalizing peptide groups and protein abundances - Proteome Discoverer Software - Proteome Discoverer Software

After the Reporter Ions Quantifier node and the Precursor Ions Quantifier node calculate the protein abundances for the samples, they normalize the peptide groups and protein abundances, impute missing values, and scale them. In general, the nodes apply the normalization of the total abundance values for each channel across all files, equalizing the total abundance between different runs.

You can use the following parameters of the Reporter Ions Quantifier node and the Precursor Ions Quantifier node to normalize peptide groups and protein abundances.