FeatureFinderMetaboIdent

Detects features in MS1 data based on metabolite identifications.

Web Documentation for 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.

Input Ports

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Input file: LC-MS raw data [mzML]
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Input file: Metabolite identifications [tsv]

Output Ports

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Output file: Features [featureXML]
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Output file: Assay library [traML]
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Output file: Chromatograms [mzML]
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Output file: Retention times (expected vs. observed) [trafoXML]
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Optional output file: Feature candidates (before filtering and model fitting). []

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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Links

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