The Thermo Scientific mass spectrometers support different duty cycle strategies for acquiring peptide fragment spectra. In a single run, the mass spectrometer can perform independent ETD and CID fragment scans or, to improve coverage of ETD fragmentation, can perform supplemental HDC or CID activations. (In recent instrument firmware, the supplemental activations are called EThcD and ETciD.)
Special Processing Workflow Nodes and Node Settings
Depending on the activation types used in acquisition, you might need to include a separate Scan Event Filter node for each type in the processing workflow. Set each Scan Event Filter node’s Activation Type appropriately.
The workflow design enables searches of fragment spectra where each branch has the appropriate search settings. For example, the ETD scans are searched with primarily c and z ions, and the CID scans are searched with b and y ions.
Special Consensus Workflow Nodes and Node Settings
No special nodes or settings required.
Further Information
The following figure shows the results of the processing workflow.