DIA results are presented similarly to Minora Feature Detector-based label-free quantification results, with the exception of the following differences:

  • How the chromatogram traces view behaves
  • New LCMS/MS Feature table for DIA and PRM analyses
  • This table is hidden by default.

The following figure shows an example of a DIA result file.

DIA result file

For DIA results, the application does not perform any chromatographic alignment and therefore elution profiles of the same peptide might appear at slightly different positions corresponding to the time the peptide eluted in each file.

Procedure

  1. Open the DIA result file.
  2. To the left of the result tables, select Select Table Visibility .
  3. The Select Visible Tables dialog box opens.
  4. In the Select Visible Tables dialog box, do the following:
  5. Select LCMS/MS Features.
  6. Select OK.
  7. Select Show Associated Tables in the bottom left corner of the result file.
  8. A second level of tables displays that includes the LCMS/MS Features table.
  9. In the second level of tables, select the LCMS/MS Features table.
  10. In the first level of tables, select the Peptide Groups table.
  11. The associated LCMS/MS Features table updates with the quantitative values for each charge state for each of the peptides.
  12. The LCMS/MS features table also shows the number of PSMs for that file for that peptide charge state, which is equivalent to the points across the peak commonly used as a metric for quantification quality.
  13. The quantitative value for each sample, for a selected peptide group, is the sum of the peak areas for all linked LCMS/MS Features.
  14. To open the Chromatogram Traces View, select View > Chromatogram Traces View.
  15. The Chromatogram Traces View updates with all associated chromatographic profiles for the LCMS/MS Features associated with that peptide group.
  16. If you select a single LCMS/MS Feature, then only a single chromatogram displays.