You already selected a consensus workflow in the New Study and Analysis dialog box. In this section, you configure some settings in the workflow nodes.


  1. In the Analysis pane, select Edit or anywhere in the Consensus Step.
  2. In the Workflow Tree section, select the Reporter Ions Quantifier node and do the following:
  3. Change the Apply Quan Value Corrections parameter to True.
  4. Change the Minimum Channel Occupancy [%] Threshold to 100.
  5. This setting rejects peptides from being used for protein quantification due to too many missing quantitative measurements. Peptides identified in only one of the two data files are ignored for quantification for this specific analysis.
  6. Change the Scaling Mode to On Controls Average.
  7. In the Protein Annotation node, select the yeast FASTA file, Saccharomyces cerevisiae.
  8. Select the Grouping & Quantification tab.
  9. In the Study Variables section, select the Yeast Strain checkbox.
  10. In the Bulk Ratio Generation pane, select the Yeast Strain: Parental checkbox, and then select Add Ratios.
  11. In the Generated Ratios pane, confirm that the following entries appear.
  12. Met6/Parental
  13. His4/Parental
  14. Ura2/Parental
  15. In the Analysis pane, select Run.
  16. The processing and consensus workflow appears in the Job Queue.