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
- Select the Workflows tab.
- In the Analysis section, select Edit or select anywhere in the Processing Step pane.
- In the Workflow Tree, select the Spectrum Files RC node, and configure its parameters as follows:
- For the Protein Database parameter, select Homo sapiens (sp_incl_isoforms TaxID=9606) (v2022-04-30).
TIP
The date that is available for the database may differ depending on when the database was downloaded.
- You added this file in Add the FASTA file to Proteome Discoverer.
- If you run a newer version of the database, your results might differ slightly.
- 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.
- Select anywhere on the window to accept the modifications.
- Select the Sequest HT node, and configure its parameters as follows:
- For the Protein Database parameter, select Homo sapiens (sp_incl_isoforms TaxID=9606) (v2022-04-30).
- 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.
- Select anywhere on the window to accept the parameters.
- 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.
- Hold the cursor over the Percolator node to view its handles.
- Select a handle of the Percolator node, and connect the node to the IMP-ptmRS node.
- The arrow snaps to the top of the IMP-ptmRS node.
- In the Workflow Tree pane, select the IMP-ptmRS node to view its parameters.
- 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.
- Save the processing workflow.