Name | Type | Default | Restrictions | Description |
centroid_percentage | float | 0.8 | min: 0 max: 1 | Percentage 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. |
optimization | string | no | no, one_dimensional, two_dimensional | If the peak parameters position, intensity and left/right widthshall be optimized set optimization to yes. |
thresholds:signal_to_noise | float | 1 | min: 0 | Minimal signal to noise ratio for a peak to be picked. |
thresholds:peak_bound | float | 10 | min: 0 | Minimal peak intensity. |
thresholds:peak_bound_ms2_level | float | 10 | min: 0 | Minimal peak intensity for MS/MS peaks. |
thresholds:fwhm_bound | float | 0.2 | min: 0 | Minimal peak width |
thresholds:correlation | float | 0.5 | min: 0 max: 1 | minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped. |
thresholds:noise_level | float | 0.1 | min: 0 | noise level for the search of the peak endpoints. |
thresholds:search_radius | int | 3 | min: 0 | search radius for the search of the maximum in the signal after a maximum in the cwt was found |
wavelet_transform:scale | float | 0.15 | min: 0 | Width of the used wavelet. Should correspond approx. to the fwhm of the peaks. |
wavelet_transform:spacing | float | 0.001 | min: 0 | spacing of the cwt. |
optimization:iterations | int | 15 | min: 1 | maximal number of iterations for the fitting step |
optimization:delta_abs_error | float | 1e-04 | min: 0 | if the absolute error gets smaller than this value the fitting is stopped. |
optimization:delta_rel_error | float | 1e-04 | min: 0 | if the relative error gets smaller than this value the fitting is stopped |
optimization:penalties:position | float | 0 | min: 0 | penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized |
optimization:penalties:left_width | float | 1 | min: 0 | penalty 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_width | float | 1 | min: 0 | penalty 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:height | float | 1 | min: 0 | penalty 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_mz | float | 2.2 | min: 0 | mz tolerance for cluster construction |
optimization:2d:max_peak_distance | float | 1.2 | min: 0 | maximal peak distance in mz in a cluster |
deconvolution:skip_deconvolution | string | yes | yes, no | If you want heavily overlapping peaks to be separated set this value to "no" |
deconvolution:asym_threshold | float | 0.3 | min: 0 | If 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_width | float | 2 | min: 0 | 1/left_width is the initial value for the left width of the peaks found in the deconvolution step. |
deconvolution:right_width | float | 2 | min: 0 | 1/right_width is the initial value for the right width of the peaks found in the deconvolution step. |
deconvolution:scaling | float | 0.12 | min: 0 | Initial 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_threshold | float | 0.7 | min: 0 | If 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_abs | float | 1e-05 | min: 0 | if the absolute error gets smaller than this value the fitting is stopped. |
deconvolution:fitting:eps_rel | float | 1e-05 | min: 0 | if the relative error gets smaller than this value the fitting is stopped. |
deconvolution:fitting:max_iteration | int | 10 | min: 1 | maximal number of iterations for the fitting step |
deconvolution:fitting:penalties:position | float | 0 | min: 0 | penalty 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:height | float | 1 | min: 0 | penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized. |
deconvolution:fitting:penalties:left_width | float | 0 | min: 0 | penalty 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_width | float | 0 | min: 0 | penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized. |