How to optimize the baseline with a morphological algorithm

The first choice when you want to optimize the peak integration is to change the baseline parameters. This section describes how to optimize the baseline with a morphological algorithm.

The Morphological algorithm can be described as a line that follows the chromatogram parallel to the X-axis. Data points for the baseline are created whenever the line touches the curve, and the points are joined at the end to create a baseline.

The Morphological algorithm gives the best result in curves with drifting baseline and peak clusters. The morphological baseline follows the curve faithfully, and a curve with a baseline at a more even level can be created by subtracting the morphological baseline.

The Morphological algorithm does not work well if there are negative peaks or if quantitative data from negative peaks are important in the run.

Note: The Morphological algorithm is the default baseline setting.

The table below describes how to choose a Morphological algorithm and define baseline settings.

Note: The same settings can be edited in the Calculate Baseline dialog box when a new baseline is created. Choose Integrate:Calculate Baseline to open the dialog box.

The parameters for the Morphological algorithm are:

• Structure width

• Noise window

• Minimum distance between points

Structure width determines the length of the straight line that follows the chromatogram. The default value is set at the widest peak in the chromatogram multiplied by 1.5.

The illustration below is an example of how a morphological baseline follows the peaks at the different levels in the curve:

Too low settings

Too low Structure width settings can result in a baseline that reaches too high up in the peaks of the curve. Sometime a wider peak is not recognized because it contains a cluster of smaller peaks. The Structure width is then set to a value according to the largest width of the identified narrower peaks, and must be increased.

Too high settings

Too high Structure width settings mean that narrower peaks, especially in fluctuating curves, are not properly followed. This happens when an artifact in a curve is identified as the widest peak by the morphological algorithm, and then is used to set the default Structure width value.

The illustration below is an example of baselines using the default morphological algorithm settings (A) and a morphological algorithm with an increased Structure width value (B).

Sometimes you get too many peaks after the peak integration, usually because noise on the baseline is erroneously detected as peaks.

The solution to this is to increase the Noise window parameter. However, this can result in peak limits too high up on the peak slopes.

Note: You can also use the Reject peaks function in the Integrate dialog box to reduce the number of peaks based on the total number of accepted peaks or the minimum peak height.

The Minimum distance between points is a measure of the distance between the data points used to generate a baseline. The largest number of data points is produced at the slopes of the curves. If you increase the Minimum distance between points value, fewer points will be collected on the slopes.

The illustration below is an example of a baseline (A) that is created with the Minimum distance between points parameter set at a low value. The number of data points is reduced when the Minimum distance between points parameter is set to a higher value (B).