FeatureFinderMetaboIdent

Options

version

Version of the tool that generated this parameters file.

force

Overrides tool-specific checks

debug

Sets the debug level

log

Name of log file (created only when specified)

threads

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

no_progress

Disables progress logging to command line

test

Enables the test mode (needed for internal use only)

mz_window

m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)

rt_window

RT window size (in sec.) for chromatogram extraction. If set, this parameter takes precedence over 'extract:rt_quantile'.

n_isotopes

Number of isotopes to include in each peptide assay.

isotope_pmin

Minimum probability for an isotope to be included in the assay for a peptide. If set, this parameter takes precedence over 'extract:n_isotopes'.

peak_width

Expected elution peak width in seconds, for smoothing (Gauss filter). Also determines the RT extration window, unless set explicitly via 'extract:rt_window'.

min_peak_width

Minimum elution peak width. Absolute value in seconds if 1 or greater, else relative to 'peak_width'.

signal_to_noise

Signal-to-noise threshold for OpenSWATH feature detection

type

Type of elution model to fit to features

add_zeros

Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; '0' to disable.

unweighted_fit

Suppress weighting of mass traces according to theoretical intensities when fitting elution models

no_imputation

If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate

each_trace

Fit elution model to each individual mass trace

min_area

Lower bound for the area under the curve of a valid elution model

boundaries

Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting

width

Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace').

asymmetry

Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace').

max_iteration

Maximum number of iterations for EMG fitting.

init_mom

Alternative initial parameters for fitting through method of moments.

Views

FeatureFinderMetaboIdent Std Output

The text sent to standard out during the execution of FeatureFinderMetaboIdent.

FeatureFinderMetaboIdent Error Output

The text sent to standard error during the execution of FeatureFinderMetaboIdent. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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