To support reporter ion quantification, you can start with one of the workflow templates that already contain it, or add the necessary nodes, as described, to the workflow.
Special Processing Workflow Nodes and Node Settings
NOTE
The Orbitrap Astral workflows for TMT are new and are required to do TMT quan for Orbitrap Astral data. The Hybrid and Tribrid workflows will not produce quan data for the Orbitap Astral.
Add a Reporter Ions Quantifier Node to the processing workflow or use a template that includes the node, such as:
PWF_Hybrid_TMT_MS2_CHIMERYS.pdProcessingWF
PWF_Hybrid_TMTpro_MS2_CHIMERYS.pdProcessing WF
PWF_Hybrid_TMT_Sequest HT_INFERYS_Rescoring_Percolator.pdProcessingWF
PWF_Hybrid_TMTpro_Sequest HT_INFERYS_Rescoring_Percolator.pdProcessingWF
PWF_Tribrid_TMT_MS2_SequestHT_Percolator.pdProcessingWF
PWF_Tribrid_TMT_Quan_SPS_MS3_SequestHT_Percolator.pdProcessingWF
PWF_Tribrid_TMT_Quan_SPS_MS3_SequestHT_INFERYS_Rescoring_Percolator.pdProcessingWF
PWF_Tribrid_TMT_SPS_MS3_RTS_Sequest HT_INFERYS Rescoring_Comet_Percolator.pdProcessingWF
PWF_Tribrid_TMTpro_Quan_SPS_MS3_SequestHT_INFERYS_Rescoring_Percolator.pdProcessingWF
PWF_Tribrid_TMTpro_Quan_SPS_MS3_SequestHT_Percolator.pdProcessingWF
PWF_Tribrid_TMTpro_SPS_MS3_RTS_Sequest HT_INFERYS Rescoring_Comet_Percolator.pdProcessingWF
PWF_Astral_TMT_CHIMERYS.pdProcessingWF
PWF_Astral_TMT_SequestHT_INFERYSRescoring_Comet.pdProcessingWF
PWF_Astral_TMTpro_CHIMERYS.pdProcessingWF
PWF_Astral_TMTpro_SequestHT_INFERYSRescoring_Comet.pdProcessingWF
Special Consensus Workflow Nodes and Node Settings
Add a Reporter Ions Quantifier Node to the consensus workflow or use a template that includes it, such as:
CWF_Comprehensive_Enhanced Annotation_Reporter_Quan_MS2.pdConsensusWF
CWF_Comprehensive_Enhanced Annotation_Reporter_Quan_MS3.pdConsensusWF.
The MS2 workflow should be used when the TMT reporter ions are quantified in the MS/MS spectrum. The MS3 workflow should be used when the TMT reporter ions are acquired using the SPS MS3 or SPS MS3 real time search methods.
Further Information
For more information on the Reporter Ions Quantifier Node, see the Reporter Ions Quantifier node in the Proteome Discoverer Help.
Proteome Discoverer 3.1 Familiarization Guide includes examples of using reporter ion quantification.