Use this method when the Ratio Calculation parameter in the Precursor Ion Quantifier and the Reporter Ions Quantifier nodes are set to Pairwise Ratio Based. For non-nested study designs, the application calculates the peptide group ratios as the geometric median of all combinations of ratios from all the replicates for the selected study factors. The protein ratio is subsequently calculated as the geometric median of the peptide group ratios. The following figure shows an example calculation of peptide group and protein ratios for a non-nested design.
For precursor ion quantification, the pairwise ratios for the peptide groups for the different isotopic forms of a given peptide are combined and displayed on only one of the isotopic forms for that peptide.
For a nested study design, the replicates are calculated as the geometric median of all the pairwise ratios for the technical replicates for the given biological replicate. The peptide sample group ratios are then calculated as the geometric median of the biological replicate ratios just as is done for the summed abundance method above. The protein ratio is then calculated as the geometric median of the peptide group ratios. The following figure shows an example calculation of peptide group and protein ratios for a nested study that contains both biological and technical replicates.
The Maximum Allowed Fold Change parameter defines the maximum fold change that the node calculates. All ratios are between 1/fold change and fold change. When the numerator or the denominator is 0, the ratio is the fold change when the denominator is 0 or 1/fold change when the numerator is 0.