You can change the Oligonucleotide Sequence Coverage Map parameters to modify the oligonucleotide recovery parameters and the number of nucleotides displayed per row.

Prerequisites

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

Procedure

  1. On the Coverage page, right-click anywhere in the Coverage Results table and select Show Oligonucleotide Coverage Map Parameters from the shortcut menu.
  2. The Coverage Map Options dialog box opens.
  3. image/svg+xml
    Coverage Map Options dialog box, shown for a peptide mapping analysis

  4. NOTE

    If you define specific components for the Oligonucleotide Sequence Coverage Map, you can update only the "Residues per Row" parameter in the Coverage Map Options dialog box.

    The other parameters are read-only.

  5. Enter the following settings:
  6. Maximum Oligonucleotide Mass: Type a value to specify the maximum oligonucleotide mass to be included in the Oligonucleotide Sequence Coverage Map.
  7. Minimum Confidence: Type a value between 0.00 and 1.00 to set the minimum confidence level for a nucleotide assignment on a 0 to 100% scale, with 1.00 being the highest confidence. The application automatically converts this value to a percentage value between 0.00% and 100.00%.
  8. If you set the Search by Full MS Only option to "Yes" in the processing method, set this value to 0.00%. Otherwise, you will not see any coverage.
  9. Residues per Row: Type the maximum number of nucleotides (residues) to display in each row of the Oligonucleotide Sequence Coverage Map.
  10. Minimum Recovery: Type a value between 0.00 and 1.00 to specify the minimum recovery threshold on a 0 to 100% scale, with 1.00 being the highest recovery. The application automatically converts this value to a percentage value between 0.00% and 100.00%.
  11. A nucleotide must have a recovery value higher than this threshold to be included in the coverage map for a nucleotide assignment.
  12. Minimum Relative Recovery of Overlapping Oligonucleotides: Type a value between 0.00 and 1.00 to specify the minimum relative abundance threshold on a 0 to 100% scale, with 1.00 being the highest threshold. The application automatically converts this value to a percentage value between 0.00% and 100.00%.
  13. A nucleotide must have a relative abundance value higher than this threshold to be included in the Oligonucleotide Sequence Coverage Map.
  14. Select OK.
  15. The Oligonucleotide Sequence Coverage Map updates based on your settings.

  16. IMPORTANT

    The parameter settings in the Coverage Map Options dialog box are not related to the chromatogram shading settings specified for the Coverage chromatogram.

    For more information on the shading settings used in the Coverage chromatogram, see Modify the shading parameters.