In the Configure automated processing chapter we described how to choose an analysis template, a quantification method, and target folders on the Ardia server for automated processing. While running data immediately post-acquisition improves data management and analysis throughput, the analysis is still performed on single files rather than a full dataset. After an automated run, there could be hundreds if not thousands of analysis results from the individual files that need to be integrated into the final report. The following topics provide guidance on how to set up automated analysis to make the study design and the multiconsensus report as straightforward as possible for larger studies.

The following are suggested steps for running large studies using automated processing:

  1. Create a Processing-only Proteome Discoverer analysis that will produce MSF files from the analysis of each raw file in the study. Use the new PSM and Protein Grouper to ensure that the MSF file reports the number of proteins, peptide groups, and PSMs at 1% FDR. See Create templates for automated processing.
  2. Queue up the runs in Xcalibur, selecting the same target Result Path for every sample from the same study. See Configure automated processing.
  3. Open or create a study in the Proteome Discoverer 3.1 application. See Create a study.
  4. Import the PD Processing results for each sample previously acquired and analyzed for the study. See Access remote files and results within a study.
  5. Create appropriate study factors and assign the study factors to the quan channels.

  6. TIP

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

  7. Select all results in the Analysis Results tab in the study and select Reprocess > Use Results to Make New (Multi) consensus.
  8. Select the default consensus workflow.
  9. Select your target ratios.
  10. Run the consensus workflow.