Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
debug | int | 0 | min: 0 max: 1 | If not 0 debug mode is activated. Then several files with intermediate results are written. |
intensity:bins | int | 10 | min: 1 | Number of bins per dimension (RT and m/z). |
mass_trace:mz_tolerance | float | 0.06 | min: 0 | m/z difference tolerance of peaks belonging to the same mass trace. |
mass_trace:min_spectra | int | 14 | min: 1 | Number of spectra the have to show the same peak mass for a mass trace. |
mass_trace:max_missing | int | 4 | min: 0 | Number of spectra where a high mass deviation or missing peak is acceptable. |
mass_trace:slope_bound | float | 0.1 | min: 0 | The maximum slope of mass trace intensities when extending from the highest peak |
isotopic_pattern:charge_low | int | 1 | min: 1 | Lowest charge to search for. |
isotopic_pattern:charge_high | int | 4 | min: 1 | Highest charge to search for. |
isotopic_pattern:mz_tolerance | float | 0.06 | min: 0 | Tolerated mass deviation from the theoretical isotopic pattern. |
isotopic_pattern:intensity_percentage | float | 10 | min: 0 max: 100 | Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present. |
isotopic_pattern:intensity_percentage_optional | float | 0.1 | min: 0 max: 100 | Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing. |
isotopic_pattern:optional_fit_improvement | float | 2 | min: 0 max: 100 | Minimal percental improvement of isotope fit to allow leaving out an optional peak. |
isotopic_pattern:mass_window_width | float | 100 | min: 1 max: 200 | Window width in Dalton for precalcuation of estimated isotope distribtions. |
feature:min_feature_score | float | 0.7 | min: 0 max: 1 | Overall score threshold for a feature to be reported. |
feature:min_seed_score | float | 0.8 | min: 0 max: 1 | Minimum score a peak has to have to be used as seed. The score is calculated as the geometric mean of intensity, mass trace score and isotope pattern score. |
feature:min_isotope_fit | float | 0.8 | min: 0 max: 1 | Minimum isotope fit quality. |
feature:min_trace_score | float | 0.5 | min: 0 max: 1 | Trace score threshold. Traces below this threshold are removed after the fit. |
Note:
Generated Tue Apr 1 15:36:40 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |