On the right side of the Component Detection page, the Chromatogram, Intact Fragmentation Source Spectrum, and Intact Deconvolution Source Spectrum areas display plots for each raw data file in the experiment, with a separate tab for each raw data file.
Chromatogram
By default, the Chromatogram area displays the total ion chromatogram (TIC) for each loaded raw data file. You can view the base peak chromatogram (BPC) by right-clicking in the Chromatogram pane and choosing Chromatogram Trace Type > BPC.
Peaks added to the Top Down Analysis experiment are displayed in colored boxes (spanning the RT range) on the chromatogram. The shaded box indicates the currently selected peak.
To select a peak, enter the appropriate RT Range in the Peak Selection area. Alternatively, select a single scan (single RT time point) or a range of averaged scans (RT range) directly on the chromatogram.
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 panes.
- Auto Zooming: Enlarges the selected RT range without changing the view displayed in the Source Spectrum panes.
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.
Zooming or scaling in the source spectrum does not change the m/z range that the deconvolution algorithm uses.
Intact Fragmentation and Intact Deconvolution Source Spectra
The Intact Fragmentation Source Spectrum area displays the MS/MS source spectrum for the currently selected (shaded) peak in the chromatogram.
The Intact Deconvolution Source Spectrum area displays the full-scan source spectrum for the currently selected (shaded) peak in the chromatogram.
For each peak selected on the left side of the Component Detection page, change the source spectra by editing the RT Range parameter in the Peak Selection area at the left side of the page or by doing one of the following in the Chromatogram pane:
- (For a single scan) Use the red crosshair cursor to select a single scan on the chromatogram.
- The source spectra panes display 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 rag the red crosshair cursor across the area of interest.
- The application calculates the average spectra for the selected interval and displays them in both source spectra panes.
Chromatogram and Source Spectrum commands
Right-clicking the Chromatogram or Source Spectra areas 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 Top Down 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. |
Chromatogram Trace Type | (For the Chromatogram area only) Selects which type of chromatogram to display in the Chromatogram pane (TIC or BPC). |