Set up the processing workflow - Proteome Discoverer Software - Set up the processing workflow - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. Select the Workflows tab.
2. Select Edit next to the Processing Step within the Analysis section.
3. Select the Spectrum Files RC node in the Workflow Tree.
4. For the Protein Database parameter, select the human FASTA file and the E. coli FASTA file.
5. These are the files you added in Add the FASTA files to Proteome Discoverer.
5. Select the Sequest HT node #4 in the Workflow Tree.
6. For the Protein Database parameter, select the human FASTA file and the E. coli FASTA file.
7. Select the Sequest HT node #8 in the Workflow Tree.
8. For the Protein Database parameter, select the human FASTA file and the E. coli FASTA file.
9. Select the Workflow Nodes tab on the lower left of the Workflow Editor.
10. Under Feature Detection & Quantification, select and drag the Minora Feature Detector node to the side of the Spectrum Files RC node in the Workflow Tree.
11. The node automatically connects to the Spectrum Files RC node.

14. NOTE

    If using the CHIMERYS workflow, you will need to choose the Human and E coli databases, ensure that inferys_2_1_fragmentation is selected for the Prediction Model, Oxidation (M) is selected as a dynamic modification, and Carbamidomethyl (C) is selected as a static modification. The Minora Feature Detector is already in the workflow and thus does not need to be added.