On the right side of the Component Detection page, the Chromatogram and Source Spectrum areas display plots for each raw data file in the experiment, with a separate tab for each raw data file.
The peak selection process depends on the selected source spectra (deconvolution) method (Sliding Windows, Auto Peak Detection, or Average Over Selected Retention Time).
Plots for Auto Peak Detection experiments
If you select the Auto Peak Detection option as the source spectra (deconvolution) method, the application uses the Parameterless Peak Detection (PPD) algorithm as the internal peak selection mechanism to automatically select chromatographic peaks. It displays these detected peaks in blue.
Plots for Sliding Windows and Average Over Selected Retention Time experiments
If you select the Sliding Windows or Average Over Selected Retention Time option as the source spectra (deconvolution) method, you must manually select the chromatogram peaks by dragging the cursor (left to right) over a retention time (RT) range.
The chromatogram mode determines the function to apply when you drag the cursor to selected an RT range. Select the chromatogram mode in the upper right corner of the Chromatogram pane:
- Averaging: Averages the spectra for all the scans in the selected RT range and displays them in the Source Spectrum pane.
- Auto Zooming: Enlarges the selected RT range without changing the view displayed in the Source Spectrum pane.
Zooming or scaling in the source spectrum does not change the m/z range that the deconvolution algorithm uses.
Additionally, for experiments using the Average Over Selected Retention Time source spectra (deconvolution) method, you must create a source spectrum by editing the RT Range parameter or by doing one of the following in the Chromatogram area:
- (For a single scan) Use the red crosshair cursor to select a single scan on the chromatogram.
- The Source Spectra area displays the associated single-scan mass spectra at that time point.
- (For multiple scans) Select a region of the chromatogram to display the averaged spectrum for all the scans within that region.
- To select a region, select the Averaging option in the Mode area and then drag the red crosshair cursor across the area of interest.
- The application calculates the average spectrum for the selected interval and displays them in the Source Spectra area.
TIP
The Averaging method is better suited for complex MS data than the single-scan method. Averaging spectra produces higher signal-to-noise ratios and optimal deconvolution results.
Chromatogram and Source Spectrum commands
Right-clicking the Chromatogram or Source Spectrum area of the Component Detection page opens a shortcut menu that contains the commands listed in the following table.
Commands | Description |
|---|---|
Reset Scale | Restores the pane to the original view. |
Copy as Displayed | Copies the image viewable in the pane to the clipboard. |
Copy per Global Settings | Copies the image in the pane to the clipboard based on the global image dimensions set in the Intact Mass Analysis Settings dialog box. |
Zoom Out | Shrinks the view in the pane by a factor of 2. |
Zoom In | Enlarges the view in the pane by a factor of 2. |