On the Process and Review page, you can view various types of chromatograms for the peaks and/or proteoforms detected in your top down analysis experiment. Each chromatogram plot displays the relative signal intensity versus retention time for the selected component.

Procedure

  1. Open the results of your experiment from the Queue page or from the Load Results page.
  2. See Open results.
  3. The Process and Review page opens by default and displays the results of your top down analysis experiment, including the chromatograms.
  4. Depending on the parameters specified in the processing method, the Chromatogram pane displays one of the following chromatograms:
  5. •Extracted ion chromatogram (XIC): Appears when the Calculate XIC checkbox is selected in the processing parameters (for Xtract deconvolution of full-scan MS data)
  6. •Total ion chromatogram (TIC): Available for all experiments.
  7. •Base peak chromatogram (BPC): Available for all experiments.
  8. See Chromatogram plot types.
  9. To change the chromatogram type displayed in the Chromatogram pane, right-click anywhere in the pane to open the shortcut menu, select Chromatogram Trace Type, and select the checkbox for the chromatogram type you want to display.
  10. See Chromatogram pane commands.
  11. The chromatogram mode determines the function to apply when you drag the cursor over a retention time area of the Chromatogram pane. Select the chromatogram mode in the upper right corner of the Chromatogram pane:
  12. Averaging: Averages the spectra for all the scans in the retention time range that you drag the cursor over (left to right) and displays them in the Source Spectrum pane.
  13. See View the source spectra.
  14. Auto Zooming: Enlarges the area (intensity and time) that you drag the cursor over without changing the view displayed in the Source Spectrum pane.
  15. Do one of the following:
  16. In the Intact Fragmentation Results table, select the row of a peak (or lower-level proteoform).
  17. In the Intact Deconvolution Results table, select a peak from the Peak Selection list in the title bar.
  18. The Chromatogram pane shows one plot (for a single loaded raw data file in the experiment) or multiple stacked plots (for multiple loaded raw data files).
  19. The chromatogram displays a red box around the retention time (RT) range specified for the selected (or upper level) peak.
  20. (Optional) Do one of the following:
  21. In the Intact Fragmentation Results table, expand (+/− icon) a peak row in the table and then select the row for a single proteoform.
  22. In the Intact Deconvolution Results table, expand (+/− icon) a component row in the table and then select the row for a single raw data file.
  23. The Chromatogram pane shows the chromatogram plot for the selected raw data file.
Chromatogram pane showing the stacked total ion chromatograms (TICs) for each raw data file in the experiment
image/svg+xml Modeoptions Raw data file name for the first plot Raw data file namefor the second plot Modeoptions Raw data file name for the first plot Raw data file namefor the second plot