MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile.
This TOPP tool detects mass traces in centroided LC-MS maps and stores them as features in a FeatureMap. These features may be either used directly as input for an metabolite ID approach or further be assembled to aggregate features according to a theoretical isotope pattern. For metabolomics experiments, the FeatureFinderMetabo tool offers both mass trace extraction and isotope pattern assembly. For proteomics data, please refer to the FeatureFinderCentroided tool.
The command line parameters of this tool are:
stty: 'standard input': Inappropriate ioctl for device
MassTraceExtractor -- Detects mass traces in centroided LC-MS data.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MassTraceExtractor.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
MassTraceExtractor <options>
This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed description or use the --helphelp option
Options (mandatory options marked with '*'):
-in <file>* Input centroided mzML file (valid formats: 'mzML')
-out <file>* Output featureXML file with mass traces (valid formats: 'featureXML', 'consensusXML')
-out_type <type> Output file type -- default: determined from file extension or content (valid: 'featureXML', 'consensusXML')
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/doxygen/nightly/html/TOPP_MassTraceExtractor.html
INI file documentation of this tool:
Legend:
required parameter
advanced parameter
+MassTraceExtractorDetects mass traces in centroided LC-MS data.
version3.4.0-pre-nightly-2024-12-16
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, *.consensusXML
out_type
output file type -- default: determined from file extension or contentfeatureXML, consensusXML
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
++++common
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).
++++mtd
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.
++++epd
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
enabledtrue
Enables/disables the chromatographic peak detection of mass tracestrue, false
1.9.1