You already selected a processing workflow in the New Study and Analysis dialog box. In this section, you configure additional parameters in the workflow nodes.

Procedure

  1. Select the Workflows tab.
  2. In the Analysis section, select Edit or select anywhere in the Processing Step pane.
  3. In the Workflow Tree, select the Spectrum Files RC node, and configure its parameters as follows:
  4. For the Protein Database parameter, select Homo sapiens (sp_incl_isoforms TaxID=9606) (v2022-04-30).
  5. TIP

    The date that is available for the database may differ depending on when the database was downloaded.

  6. You added this file in Add the FASTA file to Proteome Discoverer.
  7. If you run a newer version of the database, your results might differ slightly.
  8. For Dynamic Modification, select Phospho in the dropdown list on the left, and for the dropdown list on the right, select the S, T, and Y checkboxes.
  9. Select anywhere on the window to accept the modifications.
  10. Select the Sequest HT node, and configure its parameters as follows:
  11. For the Protein Database parameter, select Homo sapiens (sp_incl_isoforms TaxID=9606) (v2022-04-30).
  12. For Dynamic Modification, select Phospho in the dropdown list on the left, and for the dropdown list on the right, select the S, T, and Y checkboxes.
  13. Select anywhere on the window to accept the parameters.
  14. In the PTM Analysis section of the Workflow Nodes pane, select and drag the IMP-ptmRS node below the Percolator node in the Workflow Tree pane.
  15. Hold the cursor over the Percolator node to view its handles.
  16. Select a handle of the Percolator node, and connect the node to the IMP-ptmRS node.
  17. The arrow snaps to the top of the IMP-ptmRS node.
  18. In the Workflow Tree pane, select the IMP-ptmRS node to view its parameters.
  19. The default parameters are generally appropriate identification and site localization of all PTMs including phosphorylation. Refer to the application Help for a more detailed description of the parameters.
  20. Save the processing workflow.