If quantification channels are missing, you can use the parameter settings of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node in the consensus workflow to determine how the application handles this problem. Generally, imputation handles missing quantification channels, but there are options in the Reporter Ions Quantifier node and the Precursor Ions Quantifier node that you can use to include or ignore PSMs, peptide groups, or proteins that do not measure all expected quantification channels.
You can do one of the following:
- Accept spectra with missing quantification channels, report the minimum or maximum allowed fold change, and use the quantification results (for example, x/0 = 100.000, 0/x = 0.010). The default consensus quantification workflows use his option.
- Reject the quantification results.
- Replace the missing reporter with imputed abundance values.
The following topics discuss these options in more detail.