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FeatureFinderAlgorithmPicked Parameters

Parameters of FeatureFinderAlgorithmPicked:

NameTypeDefaultRestrictionsDescription
debugint0min: 0 max: 1If not 0 debug mode is activated. Then several files with intermediate results are written.
intensity:binsint10min: 1Number of bins per dimension (RT and m/z).
mass_trace:mz_tolerancefloat0.06min: 0m/z difference tolerance of peaks belonging to the same mass trace.
mass_trace:min_spectraint14min: 1Number of spectra the have to show the same peak mass for a mass trace.
mass_trace:max_missingint4min: 0Number of spectra where a high mass deviation or missing peak is acceptable.
mass_trace:slope_boundfloat0.1min: 0The maximum slope of mass trace intensities when extending from the highest peak
isotopic_pattern:charge_lowint1min: 1Lowest charge to search for.
isotopic_pattern:charge_highint4min: 1Highest charge to search for.
isotopic_pattern:mz_tolerancefloat0.06min: 0Tolerated mass deviation from the theoretical isotopic pattern.
isotopic_pattern:intensity_percentagefloat10min: 0 max: 100Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.
isotopic_pattern:intensity_percentage_optionalfloat0.1min: 0 max: 100Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.
isotopic_pattern:optional_fit_improvementfloat2min: 0 max: 100Minimal percental improvement of isotope fit to allow leaving out an optional peak.
isotopic_pattern:mass_window_widthfloat100min: 1 max: 200Window width in Dalton for precalcuation of estimated isotope distribtions.
feature:min_feature_scorefloat0.7min: 0 max: 1Overall score threshold for a feature to be reported.
feature:min_seed_scorefloat0.8min: 0 max: 1Minimum 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_fitfloat0.8min: 0 max: 1Minimum isotope fit quality.
feature:min_trace_scorefloat0.5min: 0 max: 1Trace score threshold.
Traces below this threshold are removed after the fit.

Note:


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