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required parameter
advanced parameter
+MassTraceExtractorDetects mass traces in centroided LC-MS data.
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'MassTraceExtractor'
in
input centroided mzML fileinput file*.mzML
out
output featureXML file with mass tracesoutput file*.featureXML
log
Name of log file (created only when specified)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue,false
testfalse
Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
++++common
noise_threshold_int10
Intensity threshold below which peaks are regarded as noise.
chrom_peak_snr3
Minimum signal-to-noise a mass trace should have.
chrom_fwhm5
Expected chromatographic peak width (in seconds).
++++mtd
mass_error_ppm20
Allowed mass deviation (in ppm).
reestimate_mt_sdtrue
Enables dynamic re-estimation of m/z variance during mass trace collection stage.true,false
min_sample_rate0.5
Minimum fraction of scans along the mass trace that must contain a peak.
min_trace_length5
Minimum expected length of a mass trace (in seconds).
++++epd
width_filteringoff
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.off,fixed,auto
min_fwhm3
Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto.
max_fwhm60
Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto.
masstrace_snr_filteringfalse
Apply post-filtering by signal-to-noise ratio after smoothing.false,true
min_trace_length5
Minimum length of a mass trace (in seconds).
max_trace_length300
Maximum length of a mass trace (in seconds).
enabledtrue
Enables/disables the chromatographic peak detection of mass tracestrue,false