MassTraceExtractor

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.

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

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.)

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