Baseline correction and noise elimination algorithms analyze ion profiles (selected ion chromatograms) of all ions appearing in spectra over the entire region of a chromatogram. In contrast to thresholding, where the individual scans and their spectral peaks are independently analyzed and modified, baseline correction and noise elimination analyze and modify spectral peaks in a given retention time range.

To apply baseline correction and noise elimination to your data, click on the Chromatogram Processing button and choose the Baseline pop-up menu item. The dialog window will appear with the following parameters:

Process Top Stages Only: If checked, spectra in MS1 stage (full scan) will be processed.

Segmentation: If checked, the chromatogram will be divided into discrete parts to which the algorithms are applied separately. This option can provide better results if a chromatogram exhibits diverse shape, peak density and baseline characteristics over the retention time scale. Segmentation should be avoided if a Loess derivative filter is used.

Use Baseline Correction: If checked, one of the following methods will be applied to your chromatogram: Top-Hat filter, Savitzky-Golay derivative filter, or Loess derivative filter.

Use Noise Elimination: If checked, the following methods can be applied individually or simultaneously: Counter filter to reduce chemical noise and Quantile filter to reduce electronic noise.