If one or more of the quantification channels are missing, the calculated ratios using these channels are either zero or infinity, depending on which channel is the numerator and which is the denominator. Even if all channels are present, the calculated ratios might be very high or very low.
You can use the Maximum Allowed Fold Change parameter of the Reporter Ions Quantifier node or Precursor Ions Quantifier node to replace such extremely high or extremely low ratios with the maximum or minimum allowed fold change. That is, extremely high ratios (greater than 100) are replaced by 100, and extremely low ratios (less than 0.01) are replaced by 0.01. If you set the Maximum Allowed Fold Change parameter to 1000, the application replaces any ratios higher than 1000 by 1000. It replaces any ratios less than 0.001 by 0.001. By default, the Maximum Allowed Fold Change parameter is set to 100. You can find this parameter in the General Quantification Settings category in the Parameters area. You can expect an inherent dynamic range to be valid or detectable with the given instrumentation and method.
To accept spectra with missing quantification channels, set the Reject Quan Results with Missing Channels parameter to False in the Reporter Ions Quantifier node or Precursor Ions Quantifier node.
