Thresholding is a data processing method that analyzes every scan to reduce ion intensities or delete spectral peaks if algorithmic criteria have been met. The main purpose of thresholding is to eliminate noise (high resolution) or impurity (column bleeding) peaks or peaks originating from minor components that are not of interest.

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

Apply Threshold to Top Stage Only: If checked, only MS1 (full scan) scans will be processed.

Minimal Remaining Peak Count: If checked, the number of the most intense peaks specified in the Minimal edit box will not be affected by thresholding.

Algorithmic: If checked, one of the following algorithms will be used: Linear Fit, Histogram or Median (see figures below).

Apply Threshold to Spectra with Peak Count Higher than: If checked, algorithmic thresholding will be applied to spectra with a number of peaks higher than the specified value.

Maximal Allowed Threshold: If checked, the algorithmic threshold will be applied to spectral peaks with an intensity lower than the specified value.

Manual: If checked, all peaks that exhibit an intensity lower than the value given in the Threshold edit box will be deleted.