This section describes using PCA plots and filters.

NOTE

Periodically, the FASTA files provided by the Annotation Server or UniProt are updated. The minor changes in an updated file cause minor changes in the results. The changes are not important in this context. Your results will be nearly identical.

Procedure

  1. Access the results by using one of the following methods.
  2. Select the Analysis Results tab in the study, and do one of the following:
    - Double-click the row with the result ID 1.
    - Highlight the row, and click Open Result to open the result file in a separate tab.
  4. Open the job queue by selecting Administration > Show Job Queue, and do one of the following.
    - Double-click the row in the Job Queue for the Consensus workflow that just finished
    - Highlight the row, and select Open Result to open the results in a separate tab.
  6. In Windows Explorer, find the study folder, and then double-click the result file.
  7. To perform Principal Components Analysis (PCA), do the following:
  8. Open the Report Item Distribution view by either selecting View > Distribution Charts or Report Item Distribution .
  9. Select the PCA Plots tab.
  10. Ensure that the selected Data Source is Proteins: Abundances (Normalized) and that the Center and scale option is clear.

  12. NOTE

    The difference between the samples is completely captured with the first principal component (PC1). This is probably due to the changing concentrations of the E coli proteins.

  13. Select Loadings Plot.
  15. Double-click the point at the far left of the loadings plot.
  16. The E. coli protein tryptophanase is highlighted in the proteins table.
  18. Zoom into the region from about -0.05 and -0.6 on the Loadings plot.
  19. You can do this by selecting beneath the x axis and dragging from the far-left side of the window to -0.05 as shown by the red line.
  21. Right-click the plot, and select Check all visible points.
  22. Sort the Proteins table by Checked.
  23. All checked entries are E. coli proteins, demonstrating that the changing abundances of the E coli proteins are responsible for differentiating the sample groups.
  24. Right-click the Proteins table, and select Uncheck All > In This Table.
  25. Close the Report Item Distributions charts.