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PeakPickerCWT Parameters

Parameters of PeakPickerCWT:

NameTypeDefaultRestrictionsDescription
centroid_percentagefloat0.8min: 0 max: 1Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity.
optimizationstringnono, one_dimensional, two_dimensionalIf the peak parameters position, intensity and left/right widthshall be optimized set optimization to yes.
thresholds:signal_to_noisefloat1min: 0Minimal signal to noise ratio for a peak to be picked.
thresholds:peak_boundfloat10min: 0Minimal peak intensity.
thresholds:peak_bound_ms2_levelfloat10min: 0Minimal peak intensity for MS/MS peaks.
thresholds:fwhm_boundfloat0.2min: 0Minimal peak width
thresholds:correlationfloat0.5min: 0 max: 1minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped.
thresholds:noise_levelfloat0.1min: 0noise level for the search of the peak endpoints.
thresholds:search_radiusint3min: 0search radius for the search of the maximum in the signal after a maximum in the cwt was found
wavelet_transform:scalefloat0.15min: 0Width of the used wavelet. Should correspond approx. to the fwhm of the peaks.
wavelet_transform:spacingfloat0.001min: 0spacing of the cwt.
optimization:iterationsint15min: 1maximal number of iterations for the fitting step
optimization:delta_abs_errorfloat1e-04min: 0if the absolute error gets smaller than this value the fitting is stopped.
optimization:delta_rel_errorfloat1e-04min: 0if the relative error gets smaller than this value the fitting is stopped
optimization:penalties:positionfloat0min: 0penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized
optimization:penalties:left_widthfloat1min: 0penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized.
optimization:penalties:right_widthfloat1min: 0penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized.
optimization:penalties:heightfloat1min: 0penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized.
optimization:2d:tolerance_mzfloat2.2min: 0mz tolerance for cluster construction
optimization:2d:max_peak_distancefloat1.2min: 0maximal peak distance in mz in a cluster
deconvolution:skip_deconvolutionstringyesyes, noIf you want heavily overlapping peaks to be separated set this value to "no"
deconvolution:asym_thresholdfloat0.3min: 0If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started.
deconvolution:left_widthfloat2min: 01/left_width is the initial value for the left width of the peaks found in the deconvolution step.
deconvolution:right_widthfloat2min: 01/right_width is the initial value for the right width of the peaks found in the deconvolution step.
deconvolution:scalingfloat0.12min: 0Initial scaling of the cwt used in the seperation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge.
deconvolution:fitting:fwhm_thresholdfloat0.7min: 0If the fwhm of a peak is higher than fwhm_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started.
deconvolution:fitting:eps_absfloat1e-05min: 0if the absolute error gets smaller than this value the fitting is stopped.
deconvolution:fitting:eps_relfloat1e-05min: 0if the relative error gets smaller than this value the fitting is stopped.
deconvolution:fitting:max_iterationint10min: 1maximal number of iterations for the fitting step
deconvolution:fitting:penalties:positionfloat0min: 0penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule.
deconvolution:fitting:penalties:heightfloat1min: 0penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.
deconvolution:fitting:penalties:left_widthfloat0min: 0penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.
deconvolution:fitting:penalties:right_widthfloat0min: 0penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.

Note:


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