You can perform these steps using the filters on the Proteins page or using the Volcano plot interface to define a protein list of significance. Then, you can use the new Enrichment Analysis feature in Proteome Discoverer 3.1 to determine which biological processes have been affected by the different gene knockouts.


  1. Drag the P-value slider to set the range of p-values along the y axis, or enter 0.05.
  2. To set the range of abundance values along the x axis, drag the Log2 Fold Change slider, or enter 0.5.
  3. Right-click on the volcano plot, and then select Check All Up-regulated Points.
  4. Return to the Proteins page, and sort by Checked.
  5. Select Enrichment Chart view .
  6. In the Enrichment table, change the Background dropdown to All Identifiable Proteins.
  7. In the far-left dropdown, select Reactome pathways.
  8. The enriched pathways are involved with amino acid biosynthesis and degradation as well as basic metabolism.