Use a PCA and Loading Plot to identify E.coli proteins - Proteome Discoverer Software - Use a PCA and Loading Plot to identify E.coli proteins - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. To perform Principal Components Analysis (PCA), do the following:
1. Open the Report Item Distribution view by either selecting View > Distribution Charts or Report Item Distribution .
2. Select the PCA Plots tab.
3. Ensure that the selected Data Source is Proteins: Abundances (Normalized) and that the Center and scale option is clear.
2. In the PCA Plots view, select the Loadings Plot tab.
3. Double-click the point at the far left of the Loadings Plot.
5. The E. coli protein Elongation Factor Tu 1 is highlighted in the proteins table.
4. Zoom in to the region from about -0.01 and -0.6 on the Loadings plot. You can do this by selecting beneath the x-axis and dragging from the far-left side of the window to -0.01 as shown in the following figure.
5. Right-click the plot, and select Check All Visible Points.
6. Sort the Proteins table by the Checked column.
7. All checked entries are E. coli proteins, demonstrating that the changing abundances of the E coli proteins are responsible for differentiating the sample groups.
7. Right-click the Proteins table, and select Uncheck All > In This Table.
8. Close the Report Item Distributions view.