After you set up an analysis in the Compound Discoverer application and verify the parameter settings for the Search mzVault node in the processing workflow, submit the analysis to the job queue.

Procedure

  1. If the Run button in the Analysis pane is unavailable, troubleshoot the analysis as follows:
  2. Check the Current Workflow Issues table and resolve any remaining issues.
  3. Make sure that the Files for Analysis area in the Analysis pane lists the input files you want to process.
    If this area does not list any files, do any of the following:
  4. Drag the files of interest from the Input Files page to the Files for Analysis area.
  5. Right-click a set of files on the Input Files page and then select Set as Input File.
  6. When the Run button becomes available, select it.

  7. NOTE

    The Analysis Validation Issues dialog box might open if the application encounters the following issues:

    • The processing workflow includes the Differential Analysis node (in the Post-Processing Nodes pane), but you did not select any study variables for grouping or set up any ratios.
    • The processing workflow does not include the Differential Analysis node, but you selected study variables for grouping and set up ratios.
  8. If the Validation Issues dialog box opens, do either of the following:
  9. Select Ignore if you do not want the analysis to include a differential analysis.
  10. The application submits the analysis to the run queue.
  11. Select Abort if you want the analysis to include a differential analysis.
  12. Set up the differential analysis by doing one of the following:
  13. Specify the study variables on the Study Definition page of the study by selecting the study variables for grouping and set up the ratios of interest on the Grouping & Ratios page of the analysis.

  14. NOTE

    For information about specifying the study variables, open the Study Definition page of the study and then press the F1 key. For information about setting up the study groups and ratios, open the Grouping & Ratios page of the analysis and then press the F1 key.

  15. Add the Differential Analysis node to the processing workflow by dragging the node from the Post-Processing area of the Workflow Nodes pane to the Post-Processing Nodes pane below the Workflow Tree pane.
  16. After setting up the differential analysis, select Run.
    The application submits the analysis to the run queue.