You can use a Venn diagram to compare distinct and shared identifications for up to three groups of data. The available groups depend on the processing nodes that you used to generate the data in the result file. Typically, you might want to compare the distinct and shared protein or peptide identifications between the following:

  • Different search engine nodes, for example, Sequest HT (2) and Sequest HT (8)
  • Different search engine types, for example, Sequest HT and Mascot
  • Different input files, for example, replicate A and replicate B

Procedure

  1. Select View > Distribution Charts, or select Distribution Charts .
  2. Select the Venn Diagrams tab in the Report Item Distribution dialog box.
  3. From the Data Source list, select the type of data to display.
  4. The available result categories depend on the search engine nodes used in the workflow that generated the Report Item Distribution chart.
  5. From the 1. Group list, select the first data set to compare.
  6. From the menu in the Color A box, select the color to display this data set in.
  7. From the 2. Group list, select the second data set to compare.
  8. From the menu in the Color B box, select the color to display this data set in.
  9. (Optional) From the 3. Group list, select the third data set to compare.
  10. From the menu in the Color C box, select the color to display this data set in.
  11. Select Refresh.
  12. (Optional) Hide the Options pane by selecting Auto Hide .
  13. The vertical icon shows the pane; the horizontal icon hides the pane. Point to Options to access the hidden Options pane.
  14. Use the options in the Options pane to adjust the colors, labels, and legends of the display. For information on these options, refer to Parameters on the Venn Diagrams view in the Proteome Discoverer Help.
  15. –or–
  16. In the Options pane of the Report Item Distribution chart, select Load to load the settings that you most recently saved.
  18. (Optional) To save all the settings that you have chosen, select Save in the Options pane.
  19. The new settings overwrite any previously saved settings. The application loads these new settings when you select Load.

Task

Procedure

Return the settings to the original default settings

In the Options pane of the Report Item Distribution chart, select Factory Defaults.

Copy a Venn diagram image

Procedure

  1. Right-click the image pane, and select Copy > Image.
  2. The application copies the image to the clipboard.
  3. In another application, paste the contents of the clipboard.

Copy the points in a Venn diagram as text

Procedure

  1. Right-click the image pane, and select Copy > Data.
  2. The application copies the data to the clipboard.
  3. In another application, paste the contents of the clipboard.
  4. The contents appear as text in the document.

Save a Venn diagram as an image file

Procedure

  1. Right-click the image pane, and select Export > Image As.
  2. In the Save As dialog box, locate the folder where you want to save the file, select the file type, and enter the file name.
  3. Select Save.
  4. The application creates a file containing the image.

Save the data from the Venn diagram in a text file

Procedure

  1. Right-click the image pane, and select Export > Data As.
  2. In the Save As dialog box, locate the folder where you want to save the file and enter the file name.
  3. Select Save.
  4. The application creates a file containing the count of the different areas of the chart.

Close the Report Item Distribution chart

Procedure

  1. Select Report Item Distribution icon or the “x” in the upper-right corner.
  2. The application stores the chart settings that you selected. When you reopen the chart, it displays these stored settings, if they are available.