You can save templates for automated processing in the Proteome Discoverer application. If your application is registered for automated processing, a list of these templates can be found on the Processing Templates page under the Ardia Server Management menu.

NOTE

You can create a Processing only template or a Processing plus Consensus template. For automation, Thermo Fisher Scientific recommends using a Processing only template.

The Consensus workflow should only be used if you do not intend to run multiconsensus workflows.

NOTE

Proteome Discoverer 3.1 does not support fractioned data for automation. For fractioned data, upload to the Ardia server first and then add fractions in Proteome Discoverer at a later time. Thermo Fisher Scientific will support fractioned data for automation in future releases.

Procedure

  1. Open an existing study or create a new study.
  2. Open an existing analysis or create a new analysis.
  3. Thermo Fisher Scientific recommends only using the Processing Step for automated processing.
  4. To remove the Consensus Step of the analysis, do the following:
  5. In the Analysis area of the study, select the X in the upper right corner.
  7. In the Workflow Tree, review all of the nodes and make sure there are no warnings.
  8. Select the PSM and Protein Grouper node and drag it to the Post-processing area.
  9. In the Analysis area of the study, select the Save dropdown menu.
  10. In the dropdown menu, select For Automated Processing.
  12. The Save as Automated Processing Template dialog box opens.
  13. Enter a name for the template.
  14. Select the Quan Method Type dropdown list and select a Quan Method.
  15. None: is used for DIA and LFQ
  16. Reporter Based: is used for TMT
  17. Precursor Based: is used for Silac
  18. Enter a description.
  19. Select Save.