FeatureFinderMetabo assembles metabolite features from singleton mass traces.
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
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required parameter
advanced parameter
+FeatureFinderMetaboAssembles metabolite features from centroided (LC-)MS data using the mass trace approach.
version2.6.0
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
out_chrom
Optional mzML file with chromatogramsoutput file*.mzML
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
Overrides tool-specific checkstrue,false
testfalse
Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
++++commonCommon parameters for all other subsections
noise_threshold_int10.0
Intensity threshold below which peaks are regarded as noise.
chrom_peak_snr3.0
Minimum signal-to-noise a mass trace should have.
chrom_fwhm5.0
Expected chromatographic peak width (in seconds).
++++mtdMass Trace Detection parameters
mass_error_ppm20.0
Allowed mass deviation (in ppm).
reestimate_mt_sdtrue
Enables dynamic re-estimation of m/z variance during mass trace collection stage.true,false
quant_methodarea
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_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_length5.0
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.
++++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_fwhm1.0
Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.
max_fwhm60.0
Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.
masstrace_snr_filteringfalse
Apply post-filtering by signal-to-noise ratio after smoothing.true,false
++++ffmFeatureFinder parameters (assembling mass traces to charged features)
local_rt_range10.0
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
isotope_filtering_modelmetabolites (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_13Cfalse
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_intensitiestrue
Use LOWESS intensities instead of raw intensities.false,true
report_convex_hullsfalse
Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).false,true
remove_single_tracesfalse
Remove unassembled traces (single traces).false,true
mz_scoring_by_elementsfalse
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
elementsCHNOPS
Elements assumes to be present in the sample (this influences isotope detection).