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required parameter

advanced parameter

+FeatureFinderCentroidedDetects two-dimensional features in LC-MS data.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FeatureFinderCentroided'

in input fileinput file*.mzML

out output fileoutput file*.featureXML

seeds User specified seed listinput file*.featureXML

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmAlgorithm section

debugfalse When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).true,false

++++intensitySettings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)

bins10 Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.
This parameter should be decreased, if the algorithm is used on small regions of a map.1:∞

++++mass_traceSettings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).

mz_tolerance0.03 Tolerated m/z deviation of peaks belonging to the same mass trace.
It should be larger than the m/z resolution of the instument.
This value must be smaller than that 1/charge_high!0:∞

min_spectra10 Number of spectra that have to show a similar peak mass in a mass trace.1:∞

max_missing1 Number of consecutive spectra where a high mass deviation or missing peak is acceptable.
This parameter should be well below 'min_spectra'!0:∞

slope_bound0.1 The maximum slope of mass trace intensities when extending from the highest peak.
This parameter is important to seperate overlapping elution peaks.
It should be increased if feature elution profiles fluctuate a lot.0:∞

++++isotopic_patternSettings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).

charge_low1 Lowest charge to search for.1:∞

charge_high4 Highest charge to search for.1:∞

mz_tolerance0.03 Tolerated m/z deviation from the theoretical isotopic pattern.
It should be larger than the m/z resolution of the instument.
This value must be smaller than that 1/charge_high!0:∞

intensity_percentage10 Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.0:100

intensity_percentage_optional0.1 Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.0:100

optional_fit_improvement2 Minimal percental improvement of isotope fit to allow leaving out an optional peak.0:100

mass_window_width25 Window width in Dalton for precalculation of estimated isotope distributions.1:200

abundance_12C98.93 Rel. abundance of the light carbon. Modify if labeled.0:100

abundance_14N99.632 Rel. abundance of the light nitrogen. Modify if labeled.0:100

++++seedSettings that determine which peaks are considered a seed

min_score0.8 Minimum seed score a peak has to reach to be used as seed.
The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.
If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.0:1

++++fitSettings for the model fitting

epsilon_abs0.0001 Absolute epsilon used for convergence of the fit.0:∞

epsilon_rel0.0001 Relative epsilon used for convergence of the fit.0:∞

max_iterations500 Maximum number of iterations of the fit.1:∞

++++featureSettings for the features (intensity, quality assessment, ...)

min_score0.7 Feature score threshold for a feature to be reported.
The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.0:1

min_isotope_fit0.8 Minimum isotope fit of the feature before model fitting.0:1

min_trace_score0.5 Trace score threshold.
Traces below this threshold are removed after the model fitting.
This parameter is important for features that overlap in m/z dimension.0:1

min_rt_span0.333 Minimum RT span in relation to extended area that has to remain after model fitting.0:1

max_rt_span2.5 Maximum RT span in relation to extended area that the model is allowed to have.0.5:∞

rt_shapesymmetric Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.symmetric,asymmetric

max_intersection0.35 Maximum allowed intersection of features.0:1

reported_mzmonoisotopic The mass type that is reported for features.
'maximum' returns the m/z value of the highest mass trace.
'average' returns the intensity-weighted average m/z value of all contained peaks.
'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.maximum,average,monoisotopic

++++user-seedSettings for user-specified seeds.

rt_tolerance5 Allowed RT deviation of seeds from the user-specified seed position.0:∞

mz_tolerance1.1 Allowed m/z deviation of seeds from the user-specified seed position.0:∞

min_score0.5 Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.0:1

++++debug

pseudo_rt_shift500 Pseudo RT shift used when .1:∞