Use the Automatic Processing page (Figure 33) to apply smoothing or baseline subtraction to all the plots in the active chromatogram view. You can also use this page to set the mass tolerance and precision for the current data file.
Follow these procedures to set the parameters on the Automatic Processing page:
• Setting Smoothing Area Options
• Setting Baseline Subtraction Area Options
• Setting Include Peaks Area Options
• Setting Mass Tolerance Area Options
• Setting Mass Precision Area Options
To open the Automatic Processing page for the chromatogram view
1. Open a chromatogram in an active chromatogram view of the Qual Browser window.
2. To open the Chromatogram Ranges Dialog Box (see Figure 33), do one of the following:
• Right-click a chromatogram plot in the cell and choose Ranges from the shortcut menu.
• Choose Display > Ranges.
• Click on the Qual Browser toolbar.
Tip You can set default values for mass tolerance and precision on the Mass Options page of the Xcalibur Configuration dialog box. Settings on Mass Options page affect the display of all the mass data in the Xcalibur data system. You can also set default values in the Global Mass Options dialog box. Settings in this dialog box affect the display of all the mass data in the Qual Browser window.
Use the Mass tolerance and Mass precision areas of the Automatic Processing page to set new values for the current data file.
Setting the Chromatogram Ranges and Processing Options
3. Click the Automatic Processing tab.
The Automatic Processing page opens. The default values in the Mass tolerance and Mass precision areas are set in the Global Mass Options dialog. You can override these default values by setting new values on the Automatic Processing page.
Figure 33. Automatic Processing page of the Chromatogram Ranges dialog box
Setting Smoothing Area Options
Use the Smoothing area settings to smooth all scans defined by the mass range, time range, and filter settings in the Spectrum Ranges dialog box.
To set smoothing settings
1. To turn on chromatogram smoothing, select the Enable check box. To turn off chromatogram smoothing, clear the Enable check box.
Setting the Chromatogram Ranges and Processing Options
Setting Baseline Subtraction Area Options
Use the Baseline subtraction settings to apply baseline subtraction to all chromatogram plots in the active view. This algorithm fits a smooth curve through the noise in the chromatogram and subtracts this curve from the chromatogram, leaving the peaks on a flat baseline.
To set Baseline subtraction settings
1. To turn on baseline subtraction, select the Enable check box. To turn off baseline subtraction, clear the Enable check box.
2. To choose a polynomial order, specify an order for the baseline curve in the Polynomial order box. The normal operating range is 3 to 20. For complex chromatograms, use a high polynomial order.
3. To choose a Below curve (%) value and move the baseline curve up or down in the chromatogram noise, enter a value in the Below curve box. Normal operating range for this parameter is 5 to 30%, depending on the abundance and width of peaks in the chromatogram. For more or wider peaks, increase the value.
4. To change the algorithm’s precision, adjust the setting in the Tolerance box.
5. To choose how the algorithm fits the beginning and end of the chromatogram, use the Flatten edges check box.
• To make sure the beginning and end of the plot are horizontal, select the check box.
• Clear the check box if this is not required.
6. To display the polynomial function with the chromatogram, select the Overlay graph of fitted polynomial check box. Clear the check box to hide the display.
Setting Include Peaks Area Options
The Include peaks area has only one check box. Use this setting to include or exclude the reference peaks (R) and exception peaks (E) for the mass data in all the cells in the Qual Browser window.
To set peaks area settings
To include reference and exception peaks in the chromatogram display, select the Reference and exception peaks check box. To hide reference and exception peaks, clear this check box.
Setting the Chromatogram Ranges and Processing Options
Setting Mass Tolerance Area Options
Use the Mass Tolerance area of the Automatic Processing page of the Chromatogram Ranges dialog box to specify a mass tolerance for the current data file.
To set Mass tolerance area settings
1. To use mass tolerance, select the Use user defined check box.
2. Enter a value from 0.1 to 50000.0 in the Mass Tolerance box. Select a unit type.
3. To turn off mass tolerance, clear the Use user defined check box.
Setting Mass Precision Area Options
Use the Mass precision area of the Automatic Processing page of the Chromatogram Ranges dialog box to specify a mass precision for the current data file.
To set Mass precision area settings
1. Specify the number of places after the decimal point that display in mass values in the Decimals box.
2. To save the settings and close the dialog box, click OK.
Tip You can set a default value for mass tolerance on the Mass Options page of the Xcalibur Configuration dialog box. Settings on this page affect the display of all the mass data in the Xcalibur data system. You can also set a default value for mass tolerance in the Global Mass Options dialog box. Settings in this dialog box affect the display of all the mass data in the Qual Browser window.
Tip You can set a default value for mass precision on the Mass Options page of the Xcalibur Configuration dialog box. Settings on this page affect the display of all the mass data in the Xcalibur data system. You can also set a default value for mass precision in the Global Mass Options dialog box. Settings in this dialog box affect the display of all the mass data in the Qual Browser window.