Because of ion statistical effects, measurements of intensities are more variable and therefore less accurate when the mass peaks arise from a smaller population of ions. When you perform precision quantification, you might want to filter out reporter peaks or spectra that have a variability that is too high because of ion statistical effects. However, with an Orbitrap analyzer, the intensity of a signal is not proportional to the number of ions corresponding to the signal. Instead, the number of ions is proportional to the S/N value of a peak (number_of_ions = 6 ´ S/N for D30 Orbitraps, and number_of_ions = 4 ´ S/N for D20 Orbitraps).
To filter reporter ion quantification input data that is detected from a number of ions that is too small, you use the signal-to-noise (S/N) values of the reporter ion peaks instead of their intensities to provide such a measurement when ions are acquired in the Orbitrap. You can use the settings of the Reporter Abundance Based On parameter of the Reporter Ions Quantifier node to select signal-to-noise intensity values. For information on this parameter, see the Precursor Ions Quanifier node Help topic.