The Precursor Ions Quantifier node in the Consensus Workflow first validates the LC/MS features. It determines whether they contain valid values or consist only of a single peak. In addition, it marks them as shared when they are connected to multiple PSMs. The node creates a Quan Info column for the LCMS Features page that displays the following values:
- Rejected by Method: Indicates that the peptide was not used in the quantification.
The node also creates a Quan Result ID column for the Peptide Groups page, which shows an integer. Peptide Groups belonging to the same quantification result with different states have the same quantification result identifications. The node also ensures that all consensus features of a quantification result are connected to all the different peptide groups of this quantification result.
In the next step, the Precursor Ions Quantifier node validates consensus features and calculates the quantification values for the different files. It checks which LC/MS features can be used and excludes invalid features. It then creates two columns, Quan Info and Quan Info Details, for the Consensus Features page, showing the following values: (The Quan Info Details column is hidden and only shows information about why a quantification result is labeled Rejected by Method.)
- No Quan Values: Indicates that no valid features are associated with a consensus feature.
- Unknown Quan Result: Indicates that no quantification result identification could be assigned.
- Shared: Indicates that multiple peptide groups are associated with a consensus feature.
A consensus feature shows the abundances of the retention times and m/z values across different spectrum files used in the processing step. For calculating abundances, the Precursor Quantifier node sums areas of associated LC/MS features for the different files.