1. Select the Workflows tab.
  2. Select Edit next to the Processing Step within the Analysis section.
  3. Select the CHIMERYS 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 file to Proteome Discoverer.
  6. NOTE

    If using the CHIMERYS workflow, you will need to choose the Human and E coli databases, ensure that inferys_3_0_fragmentation is selected for the Prediction Model, Oxidation (M) is selected as a dynamic modification, and Carbamidomethyl (C) is selected as a static modification.