FeatureFinderMetabo

Options

version

Version of the tool that generated this parameters file.

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

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

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

noise_threshold_int

Intensity threshold below which peaks are regarded as noise.

chrom_peak_snr

Minimum signal-to-noise a mass trace should have.

chrom_fwhm

Expected chromatographic peak width (in seconds).

mass_error_ppm

Allowed mass deviation (in ppm).

reestimate_mt_sd

Enables dynamic re-estimation of m/z variance during mass trace collection stage.

quant_method

Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace.

trace_termination_criterion

Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold.

trace_termination_outliers

Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.

min_sample_rate

Minimum fraction of scans along the mass trace that must contain a peak.

min_trace_length

Minimum expected length of a mass trace (in seconds).

max_trace_length

Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.

enabled

Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection.

width_filtering

Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.

min_fwhm

Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.

max_fwhm

Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.

masstrace_snr_filtering

Apply post-filtering by signal-to-noise ratio after smoothing.

local_rt_range

RT range where to look for coeluting mass traces

local_mz_range

MZ range where to look for isotopic mass traces

charge_lower_bound

Lowest charge state to consider

charge_upper_bound

Highest charge state to consider

report_summed_ints

Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.

enable_RT_filtering

Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..

isotope_filtering_model

Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.

mz_scoring_13C

Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.).

use_smoothed_intensities

Use LOWESS intensities instead of raw intensities.

report_convex_hulls

Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).

remove_single_traces

Remove unassembled traces (single traces).

mz_scoring_by_elements

Use the m/z range of the assumed elements to detect isotope peaks. A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'

elements

Elements assumes to be present in the sample (this influences isotope detection).

Views

FeatureFinderMetabo Std Output

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

FeatureFinderMetabo Error Output

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

Workflows

• DIAMetAlyzer_2.0OpenMS
• DIAMetAlyzer_2.0KNIME Hub
• DIAMetAlyzer_ABKNIME Forum
• KNIME_GNPSExportKNIME Hub
• Metabolite_Adduct_GroupingOpenMS
• Metabolite_Adduct_GroupingKNIME Hub
• Metabolite_DeNovoIDOpenMS
• Metabolite_DeNovoIDKNIME Hub
• Metabolite_IDOpenMS
• Metabolite_IDKNIME Hub
• Metabolite_SpectralIDKNIME Forum
• Metabolomics (Accurate Mass Search only)KNIME Hub
• metabonomicsKNIME Forum
• metabonomics2021.7.30KNIME Forum

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