After normalization, the Reporter Ions Quantifier node and the Precursor Ions Quantifier node scale the optionally normalized and imputed abundances if you set its Scaling Mode parameter to On All Average or On Controls Average. By default, the nodes do not scale abundances.
- On All Average: After aggregating all the abundance or normalized abundance values per sample, the nodes scale the abundance values of each sample so that the average of all samples is 100.
- On Controls Average: After aggregating all the abundance or normalized abundance values per sample, the nodes scale the abundance values of each sample so that the average of all control samples is 100 and then scale all other samples up or down relative to 100. When you use multiplexed files, the nodes process the samples from each file separately.
The application displays normalized abundances in the Abundances (Normalized) column and scaled abundances in the Abundances (Scaled) column. The Abundances (Normalized) column appears on the Proteins and Peptide Groups pages of the result file when you set the Normalization Mode parameter of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node to Total Peptide Amount or Specific Protein Amount. The Abundances (Scaled) column appears on the same pages when you set the Scaling Mode parameter of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node to On All Average or On Controls Average. These columns do not appear if you do not apply normalization and scaling.