Study factors are usually created and assigned to quan channels prior to running the combined Processing and Consensus workflows. However, it is possible to assign study factors to data that has already been processed. When study factors have changed, only the consensus workflow will need to be (re)run to produce the ratios and corresponding ratios and statistics.

The first step to create the multiconsensus report is to add the PD processing results from the automated analysis.

Procedure

  1. Open or create a study.
  2. Select Add Files > Add Remote Results.
  3. The Pick Documents dialog box opens.
  5. Assuming that you stored all of the files in the same target folder in the Results Path column of the Xcalibur data system, select the checkboxes for all of the result files that you want to add.
  7. Select Open.
  8. Each result file is added to the Analysis Results page of the study.
  9. (Optional) If a TMT method or precursor-based quan method is required, do the following:

  10. TIP

    Refer to the Proteome Discoverer 3.1 Familiarization Guide for examples on how to create study factors and quan methods.

  11. Select the Study Definition tab and create the quan method.
  12. Select the Input Files tab and in the Quan Method column, select a quan method.
  13. (Optional) If you need to assign study factors, do the following:
  14. Select the Study Definition tab and create the study factors.
  15. Select the Samples tab and in the Study factors column, select the study factors.
  16. On the Analysis Results page, hold down Ctrl or Shift and select all of the result files needed for reprocessing.
  17. Select Reprocess > Use Results to Create New (Multi) Consensus.
  19. To load a Consensus workflow, do the following:
  20. Select a consensus workflow based on the type of quantitative method used (for example, DIA, Precursor quan/LFQ, or TMT).
  21. In the Workflow Tree, configure the parameters in the quantifier node (Precursor Ions Quantifier, Reporter Ions Quantifier, or Fragment Ions Quantifier) and Protein Annotation nodes.
  22. Select the Grouping & Quantification tab in the study and do the following:
    - In the Study Variables area, select the study factor(s) to be used to create ratios.
    - Create the ratios to be shown in the final report.
    - Select Run to run the consensus workflow.