| OpenMS 2.5.0

FeatureFinderMetabo

FeatureFinderMetabo assembles metabolite features from singleton mass traces.

pot. predecessor tools | FeatureFinderMetabo | pot. successor tools
PeakPickerHiRes | TextExporter
PeakPickerWavelet

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 (optional), 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.

Mass trace clustering can be done using either 13C distances or a linear model (Kenar et al) – see parameter 'ffm:mz_scoring_13C'. Generally, for lipidomics, use 13C, since lipids contain a lot of 13C. For general metabolites, the linear model is usually more appropriate. To decide what is better, the total number of features can be used as indirect measure

- the lower(!) the better (since more mass traces are assembled into single features). Detailed information is stored in the featureXML output: it contains meta-values for each feature about the mass trace differences (inspectable via TOPPView). If you want this in a tabular format, use TextExporter, i.e.,
  TextExporter.exe -feature:add_metavalues 1 -in <ff_metabo.featureXML> -out <ff_metabo.csv>
  By default, the linear model is used.

The command line parameters of this tool are:

    FeatureFinderMetabo -- Assembles metabolite features from centroided (LC-)MS data using the mass trace approa

    ch.

    Full documentation: http://www.openms.de/documentation/TOPP_FeatureFinderMetabo.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    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')

      -out_chrom <file>  Optional mzML file with chromatograms (valid formats: 'mzML')

    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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/TOPP_FeatureFinderMetabo.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+FeatureFinderMetabo Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'FeatureFinderMetabo'
in Centroided mzML file input file*.mzML
out FeatureXML file with metabolite features output file*.featureXML
out_chrom Optional mzML file with chromatograms output file*.mzML
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Algorithm parameters section
++++common Common parameters for all other subsections
noise_threshold_int 10.0 Intensity threshold below which peaks are regarded as noise.
chrom_peak_snr 3.0 Minimum signal-to-noise a mass trace should have.
chrom_fwhm 5.0 Expected chromatographic peak width (in seconds).
++++mtd Mass Trace Detection parameters
mass_error_ppm 20.0 Allowed mass deviation (in ppm).
reestimate_mt_sd true Enables dynamic re-estimation of m/z variance during mass trace collection stage.true,false
quant_method area 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.area,median,max_height
trace_termination_criterion outlier 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_outliers 5 Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.
min_sample_rate 0.5 Minimum fraction of scans along the mass trace that must contain a peak.
min_trace_length 5.0 Minimum expected length of a mass trace (in seconds).
max_trace_length-1.0 Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.
++++epd Elution Profile Detection (to separate isobaric Mass Traces by elution time).
enabled true Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection.true,false
width_filtering fixed 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_fwhm 3.0 Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.
max_fwhm 60.0 Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.
masstrace_snr_filtering false Apply post-filtering by signal-to-noise ratio after smoothing.true,false
++++ffm FeatureFinder parameters (assembling mass traces to charged features)
local_rt_range 10.0 RT range where to look for coeluting mass traces
local_mz_range 6.5 MZ range where to look for isotopic mass traces
charge_lower_bound 1 Lowest charge state to consider
charge_upper_bound 3 Highest charge state to consider
report_summed_ints false Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.false,true
enable_RT_filtering true Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..false,true
isotope_filtering_model metabolites (5% RMS) 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.metabolites (2% RMS),metabolites (5% RMS),peptides,none
mz_scoring_13C false 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.).false,true
use_smoothed_intensities true Use LOWESS intensities instead of raw intensities.false,true
report_convex_hulls false Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).false,true
remove_single_traces false Remove unassembled traces (single traces).false,true
mz_scoring_by_elements false 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'false,true
elements CHNOPS Elements assumes to be present in the sample (this influences isotope detection).