View the distribution of protein ratios using scatter plots - Proteome Discoverer Software - View the distribution of protein ratios using scatter plots - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. Select Report Item Distribution View .
2. Select the Scatter Plots tab, and do the following:
1. For the Data Source, select Proteins.
2. For the X Data, select Abundance Ratios (15)/(10).
3. For the Y Data, select Score Sequest HT: Sequest HT.
4. Select Refresh to the right of the Data Source above the plot.
5. The plot appears similar to the following image, where the bulk of the protein ratios are on the far-left side of the plot due to a few outliers.
3. Zoom the x axis by selecting and dragging from about 0 to 5 below the axis.
5. There are two distributions of protein ratios in this plot.
   - The dots highlighted in blue are those that are the E. coli proteins produced from filtering data in Use the display filter to view E. coli proteins.
   - The proteins with gray triangles at a ratio of 1 are the human proteins in the sample.
4. Close the Report Item Distribution View.