To support precursor ion quantification, you can start with one of the workflow templates that already contain it, or add the following nodes to a workflow.
Special Processing Workflow Nodes and Node Settings
For Precursor Ion Quantification, the application matches quantification results to peptide identification in the processing workflow using the Minora Feature Detector node. The application quantifies all features in the sample regardless of whether or not it was first identified.
Special Consensus Workflow Nodes and Node Settings
The consensus workflow must include the Feature Mapper and Precursor Ions Quantifier nodes. You can add these nodes to another consensus workflow or use a template that includes them, such as:
CWF_Comprehensive_Enhanced Annotation_LFQ_and_Precursor_Quan.pdConsensusWF
By default, precursor ion quantification uses the height of the most abundant peak at the apex of the chromatographic profile instead of the integrated peak area. You can change this setting in the Precursor Ions Quantifier node in the Consensus workflow.
Further Information
For information on the Minora algorithm, see Minora Feature Detector node.
For more information on the nodes, see the Minora Feature Detector node, the Feature Mapper node, and the Reporter Ions Quantifier node in the Proteome Discoverer Help.
Proteome Discoverer 3.1 Familiarization Guide includes an example of using precursor ion quantification.