The Precursor Ions Quantifier node 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, which is hidden by default. The column displays the following values:

  • No Quan Values: Indicates that the feature area is 0.
  • Rejected by Method: Indicates that the peptide was not used in the quantification.
  • Single Peak: Indicates that the feature consists of only a single LC/MS peak and that single peak features should not be used.
  • Missing Replicates: Indicates that not enough replicate files have detected features.
  • Shared: Indicates that different PSMs are associated with a feature.

The node also creates a Quan Channel column for the Peptide Groups page and the PSMs page, where the channel name of its labeling state is shown. 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 labeling 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. The node 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. (The Quan Info Details column is hidden and only shows information about why a quantification result is labeled Rejected by Method.) The Quan Info column and the Quan Info Details column can show one of these values:

  • No Quan Values: Indicates that no valid features are associated with a consensus feature.
  • Has Missing Values: Indicates that not all expected labeling states for a consensus feature group are available, that the Reject Quan Results with Missing Channels parameter of the Precursor Ions Quantifier node is set to True, and that no imputation is used. This value appears only when labeling was used.
  • Rejected by Method (only when labeling was used): Indicates that the peptide was not used in the quantification.
  • Unknown Quan Channel: Indicates that no channel could be assigned.
  • Unknown Quan Result: Indicates that no quantification result identification could be assigned.
  • Shared: Indicates that multiple peptide groups are associated with a consensus feature.

NOTE

The node checks for missing values and unknown quantification channels after you specify the quantification usage of consensus features for peptide groups and assign quantification channels and quantification results to the consensus features.

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.