IconMassTraceExtractor0 ×

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Detects mass traces in centroided LC-MS data.

Web Documentation for MassTraceExtractor

Options

version
Version of the tool that generated this parameters file.
out_type
output file type -- default: determined from file extension or content
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
Overwrite 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.
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.
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.
enabled
Enables/disables the chromatographic peak detection of mass traces

Input Ports

input centroided mzML file [mzML]

Output Ports

output featureXML file with mass traces [featureXML,consensusXML]

Views

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

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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