Performing TMT Quantification on HCD and CID Scans - Proteome Discoverer Software - Performing TMT Quantification on HCD and CID Scans - Proteome Discoverer Software - Proteome Discoverer Software

If a raw data file contains both CID scans for identification and HCD scans for quantification, you can quantify the HCD scans and identify peptides in the CID scans, the HCD scans, or both.

Special Processing Workflow Nodes and Node Settings

Add the Reporter Ions Quantifier node and the Spectrum Selector node to workflow, or start with a workflow template that contains them, such as:

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_SPS_MS3_RTS_Sequest HT_INFERYS Rescoring_Comet_Percolator.pdProcessingWF

Use the following parameters:

• The Reporter Ions Quantifier node, set the Activation Type parameter to HCD.
• The Spectrum Selector node, set the Activation Type parameter to Any, Is CID, HCD, or Is CID.

Special Consensus Workflow Nodes and Node Settings

No special nodes or settings required.

Further Information

For more information on the Reporter Ions Quantifier Node, see the Reporter Ions Quantifier node in the Proteome Discoverer Help.