On the Process and Review page, you can view various types of chromatograms for the components detected in your intact mass 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 intact mass analysis experiment, including the chromatograms.
  4. Depending on the Chromatogram Trace Type specified in the processing method (see Chromatogram Parameters area parameters), the Chromatogram pane displays one or more 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): Appears when TIC is selected as the Chromatogram Trace Type in the processing parameters.
  7. •Base peak chromatogram (BPC): Appears when BPC is selected as the Chromatogram Trace Type in the processing parameters.
  8. See Chromatogram plot types and Chromatogram pane commands.

  9. TIP

    For intact mass analysis experiments, you can quickly change whether the Chromatogram pane displays the TIC or BPC for the selected component by updating the Chromatogram Trace Type parameter using the real-time optimization (RTO) feature on the Process and Review page.

    See Use real-time optimization (RTO) to reprocess results.

  10. For auto peak detection experiments, the auto detected peaks are shaded in blue in the chromatogram.
  11. For sliding windows experiments, an abundance trace appears underneath the chromatogram, displaying the abundance for a selected component within the chromatogram. See Abundance traces.
  12. Select the chromatogram mode in the upper right corner of the Chromatogram pane. The chromatogram mode determines the function to apply when you drag the cursor over a retention time area of the Chromatogram pane.
  13. 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. 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. Select the row of a component in the Results table.
  16. 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).
  17. The chromatogram displays a red box around the retention time (RT) range specified for the selected component.
  18. (Optional) Expand (+/− icon) a component row in the table and then select the row for a single raw data file.
  19. The Chromatogram pane shows the chromatogram plot for the selected raw data file.
  20. image/svg+xml
    Chromatogram pane showing the stacked total ion chromatograms (TICs) for each raw data file in the experiment
Chromatogram pane showing the XIC for a selected component.
image/svg+xml Extracted ion chromatogram
Chromatogram pane showing the abundance trace for a selected m/z value.
image/svg+xml Abundancetrace