In this tutorial, the ratios were selected when creating the initial study. Each of the preceding tutorials includes an example of using study factors to create ratios and set up the statistical analysis.


  1. In the Study, select the Grouping and Quantification tab.
  2. In the Study Variables pane, select Quan Channel.
  3. In the Manual Ratio Generation pane, do the following:
  4. Select (Medium) as the Numerator, and select (Light) as the denominator, and select Add Ratio.
  5. Change the Numerator to (Heavy), and select Add Ratio.
  6. In the Analysis pane, select Run.
  7. This sample does not produce sufficient protein identifications for the statistical analysis to produce p-values for protein expression ratios. The low number of identifications triggers a warning in the consensus workflow, which states that p-values could not be calculated. However, the workflow will still complete successfully and produce ratios for peptides and proteins.