Creating Label-Free Workflows - Proteome Discoverer Software - Creating Label-Free Workflows - Proteome Discoverer Software - Proteome Discoverer Software

To support label-free quantification, that is, the quantification of MS peptide signals in LC/MS2 data without an isotopic labeling reagent, include the following nodes in your workflows.

Special Processing Workflow Nodes and Node Settings

The processing workflow must include the Minora Feature Detector node. You can add this node to a workflow or use a template that includes it, such as:

PWF_Hybrid_Precursor_Quan_and_LFQ_MPS_SequestHT_Percolator.pdProcessingWF

PWF_Hybrid_Precursor_Quan_and_LFQ_SequestHT_Percolator.pdProcessingWF

PWF_Hybrid_LFQ_CHIMERYS.pdProcessingWF

PWF_Tribrid_LFQ_CHIMERYS_ITHCD_CID.pdProcessingWF

PWF_Tribrid_LFQ_CHIMERYS_OTHCD.pdProcessingWF

PWF_Tribrid_Precursor_Quan_and_LFQ_ITHCD_CID_SequestHT_Percolator.pdProcessingWF

PWF_Tribrid_Precursor_Quan_and_LFQ_OT_CID_HCD_SequestHT_Percolator.pdProcessingWF

PWF_OT_Precursor_Quan_and_LFQ_CID_SequestHT_Percolator.pdProcessingWF

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, label-free 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 more information on the nodes, see the Minora Feature Detector node, the Feature Mapper node, and the Precursor Ions Quantifier node in the Proteome Discoverer Help.

Proteome Discoverer 3.1 Familiarization Guide includes an example of using label-free quantification.