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FeatureFinderMetabo

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.

Web Documentation for 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).

Input Ports

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Centroided mzML file [mzML]

Output Ports

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FeatureXML file with metabolite features [featureXML]
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Optional mzML file with chromatograms [mzML]

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2
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