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FeatureFinderMetabo

FeatureFinderMetabo assembles metabolite features from singleton mass traces.

pot. predecessor tools $ \longrightarrow $ FeatureFinderMetabo $ \longrightarrow $ pot. successor tools
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Mass traces alone would allow for further analysis such as metabolite ID or statistical evaluation. However, in general, monoisotopic mass traces are accompanied by satellite C13 peaks and thus may render the analysis more difficult. FeatureFinderMetabo fulfills a further data reduction step by assembling compatible mass traces to metabolite features (that is, all mass traces originating from one metabolite). To this end, multiple metabolite hypotheses are formulated and scored according to how well differences in RT and m/z or intensity ratios match to those of theoretical isotope patterns.

If the raw data scans contain the scan polarity information, it is stored as meta value "scan_polarity" in the output file.

The command line parameters of this tool are:

FeatureFinderMetabo -- Assembles metabolite features from singleton mass traces.
Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND

Usage:
  FeatureFinderMetabo <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*        Centroided mzML file (valid formats: 'mzML')
  -out <file>*       FeatureXML file with metabolite features (valid formats: 'featureXML')
                     
                     
Common TOPP options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+FeatureFinderMetaboAssembles metabolite features from singleton mass traces.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'FeatureFinderMetabo'
in Centroided mzML fileinput file*.mzML
out FeatureXML file with metabolite featuresoutput 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
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
++++commonCommon parameters for all other subsections
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).
++++mtdMass Trace Detection parameters
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
trace_termination_criterionoutlier 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.outlier,sample_rate
trace_termination_outliers5 Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.
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).
max_trace_length300 Minimum expected length of a mass trace (in seconds).
++++epdElution Profile Detection (to separate isobaric Mass Traces by elution time).
enabledtrue Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection.true,false
width_filteringfixed 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
++++ffmFeatureFinder parameters (assembling mass traces to charged features)
quant_methodarea Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data.area,median
local_rt_range10 RT range where to look for coeluting mass traces
local_mz_range6.5 MZ range where to look for isotopic mass traces
charge_lower_bound1 Lowest charge state to consider
charge_upper_bound3 Highest charge state to consider
report_summed_intsfalse Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.false,true
enable_RT_filteringtrue Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..false,true
disable_isotope_filteringfalse Disable isotope filtering.false,true
isotope_modelmetabolites Change type of isotope model.metabolites,peptides
isotope_noisemodel5%RMS SVM isotope models were trained with either 2% or 5% RMS error. Select the appropriate noise model according to the quality of measurement or MS device.5%RMS,2%RMS
use_smoothed_intensitiestrue Use LOWESS intensities instead of raw intensities.false,true

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:31 using doxygen 1.8.9.1