Procedure

  1. Select Edit or select anywhere in the Consensus Step within the Analysis section.
  2. In the Workflow Tree, select the Reporter Ions Quantifier node.
  3. For the Apply Quan Value Corrections parameter dropdown list, select True.
  4. Select the PSM Grouper node.
  5. You can accept the default 75% site localization threshold, which is generally appropriate for viewing high-confidence site IDs.
  6. In the PTM Analysis pane, select and drag the Modification Sites node into the Workflow Tree pane.
  7. Select and drag the Peptide Isoform Grouper node from the PTM Analysis section to the Workflow Tree.
  8. The arrows automatically connect to the correct nodes, but they cross over existing nodes.
  9. In the Workflow Tree, select the Protein Annotation node.
  10. In the Protein Database category, select Homo sapiens (sp_incl_isoforms TaxID=9606) (v2020-04-30).
  11. To clean up the workflow layout, select Auto Layout.