You can change the shading parameters for the Coverage chromatogram, including the shading colors assigned to each oligonucleotide in your experiment.

Prerequisites

  1. You have loaded the experiment results are viewing the Coverage page under the Mapping tab.

Procedure

  1. Right-click anywhere in the Coverage Results table and select Shading Parameters from the shortcut menu.
  2. The Shading Parameters dialog box opens.
  3. Shading Parameters dialog box
    Shading Parameters dialog box
  4. Enter the following parameters:
  5. Mass Area Threshold: Type a number for the minimum area threshold.
  6. The application does not display peaks with areas below this threshold in the chromatogram.
  7. Charge States: Type the minimum and maximum values for the range of charge states to display in the chromatogram.
  8. Maximum Mass Error (ppm): Type a value (in ppm) for the maximum mass difference (between the Theor. Mass and Mono Mass Exp.) threshold.
  9. The chromatogram does not display any peaks for an identified component with a mass error above this threshold.
  10. Identification Types: Select the checkboxes to view only the components identified by the selected identification types. This selection affects the components displayed in the Coverage chromatogram and at the component level in the Coverage Results table.

  11. TIP

    To view only unidentified components in the Coverage chromatogram, select only the "None" checkbox as the Identification Type.

  12. Oligonucleotide Color Assignment table: Use the drop-down color menu to select a shading color for a particular oligonucleotide. Select or clear the "Inc" (Include) checkbox for a particular oligonucleotide if you want to show or hide the oligonucleotide row in the Coverage Results table and its corresponding shading in the Coverage chromatogram. You can select or clear multiple checkboxes as needed.

  13. IMPORTANT

    The Coverage chromatogram shading settings are not related to the color-coding displayed in the Oligonucleotide Sequence Coverage Map.

    For more information on the color-coding used in the Oligonucleotide Sequence Coverage Map, see View the Oligonucleotide Sequence Coverage Map.

  14. Select Apply.
  15. The chromatogram updates based on your settings.