When you reject any quantification results from spectra with missing quantification channels, the application does not use the corresponding Quan Spectra to calculate the protein and peptide quantification values. The Peptide Quan Usage column of the result report displays “Not Used,” and the Quan Info column displays “No Quan Values.”
You can use the Reject Quan Results with Missing Channels parameter of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node to reject the quantification measurement if any of the quantification channels are zero. When you set this parameter to True, the application does not use a quan spectrum or consensus feature for calculating peptide group and protein quantification values if one or more of the quantification channels have a detected abundance of zero. If you set it to False, which is the default, the application calculates and displays the quantification values for those channels that it found and retains the missing channels.