OpenMS
2.5.0
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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.
The command line parameters of this tool are:
BaselineFilter -- Removes the baseline from profile spectra using a top-hat filter. Full documentation: http://www.openms.de/documentation/TOPP_BaselineFilter.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. Usage: BaselineFilter <options> Options (mandatory options marked with '*'): -in <file>* Input raw data file (valid formats: 'mzML') -out <file>* Output raw data file (valid formats: 'mzML') -struc_elem_length <size> Length of the structuring element (should be wider than maximal peak width - see documentation). (default: '3.0') -struc_elem_unit <unit> Unit of 'struc_elem_length' parameter. (default: 'Thomson' valid: 'Thomson', 'DataPoints') -method <string> The name of the morphological filter to be applied. If you are unsure, use the default. (default: 'tophat' valid: 'identity', 'erosion', 'dilation', 'opening', 'closing', 'gradient', 'tophat', 'bothat', 'erosion_simple', 'dilation_simple') Common TOPP options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced)
INI file documentation of this tool: