OpenMS
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BaselineFilter

Executes the top-hat filter to remove the baseline of an MS experiment.

pot. predecessor tools → BaselineFilter → pot. successor tools
NoiseFilterSGolay,
NoiseFilterGaussian
PeakPickerWavelet,
PeakPickerHiRes
(or ID engines on MS/MS data)

This nonlinear filter, known as the top-hat operator in morphological mathematics (see Soille, ''Morphological Image Analysis''), is independent of the underlying baseline shape. It is able to detect an over brightness even if the environment is not uniform. The principle is based on the subtraction of a signal from its opening (erosion followed by a dilation). The size the structuring element (here a flat line) being conditioned by the width of the lineament (in our case the maximum width of a mass spectrometric peak) to be detected.

Note
The top-hat filter works only on roughly uniform data! To generate equally-spaced data you can use the Resampler.
The length (given in Thomson) of the structuring element should be wider than the maximum peak width in the raw data.

The command line parameters of this tool are:

INI file documentation of this tool: