You can specify the minimum oligonucleotide and charge state intensity thresholds for detected modifications reported in the Modifications Results table.

Prerequisites

  1. You have loaded the experiment results and are viewing the Modification Summary page under the Mapping tab.

Procedure

  1. On the Modification Summary page, right-click anywhere in the Modification Results table and select Set Summary Options on the shortcut menu.
  2. The Summary Options dialog box opens.
  3. Summary Options dialog box
    Summary Options dialog box
  4. In the Oligo Minimum Intensity box, type a value to define the threshold value for the minimum nucleotide peak intensity (as a percentage of the most abundant oligonucleotide signal) that the application reports in the Modification Summary.
  5. Occasionally, an oligonucleotide might cleave unexpectedly, causing one or more sequences to appear as a modification.
  6. When the application interprets the experiment data to detect and identify modifications, an improper % Abundance calculation may result if the false modification is included.
  7. To avoid this problem, the application does not include oligonucleotide identifications whose total peak area is below a specified percentage of the most abundant signal. This filter results in the removal of less abundant identifications from the calculation.
  8. In the Charge State Minimum Intensity box, type a value to define the threshold value for the minimum charge state peak intensity (as a percentage of the most abundant charge state signal) that the application reports in the Modification Summary.
  9. When there is a large variation in signal intensities, the % Abundance calculation might underestimate the low-abundance identifications.
  10. To avoid this problem, the application does not include charge states whose abundances are below ma specified percentage of the most abundant charge state signal. This filter results in the removal of less abundant charge states from the calculation.
  11. See Change the percent abundance calculation.
  12. In the Minimum Modification Level box, type threshold value for the minimum modification level (as a percentage of the total number of components in the experiment sample) that the application reports in the Modification Summary.
  13. Select OK.
  14. The Modification Summary page updates to reflect the modification detection threshold settings.